Compositions and methods for detecting bv-associated bacterial nucleic acid

ABSTRACT

Disclosed are nucleic acid oligomers, including amplification oligomers, capture probes, and detection probes, for detection of a 16S rRNA or its encoding gene from bacterial species associated with bacterial vaginosis. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.14/113,880, filed Oct. 25, 2013, which is a section '371 National Stagefiling of PCT/US2012/035019, filed Apr. 25, 2012, which claims priorityunder 35 U.S.C. §119(e) to U.S. Provisional App. No. 61/478,753 filed onApr. 25, 2011, the entire contents of each are incorporated herein byreference.

BACKGROUND

Bacterial vaginosis (BV) is a common condition affecting millions ofwomen annually and associated with serious health problems such aspreterm labor resulting in low birth weight, pelvic inflammatorydisease, and increased risk of human immunodeficiency virus infection.See, e.g., Bodner-Adler et al., Am. J. Obstet. Gynecol. 189:139-47,2003; Hillier et al., Clin. Infect. Dis. 20:Suppl 2:S276-S278, 1995;Peipert et al.,i Am. J. Obstet. Gynecol. 184:856-63, 2001; Hillier etal., Am. J. Osbstet. Gynecol. 175:435-41, 1996; Martin et al., J.Infect. Dis. 180:1863-1868, 1999; Sturm-Ramirez et al., J. Infect. Dis.182:467-473, 2000. No single etiologic agent has been implicated as thecause of bacterial vaginosis, and the syndrome is currently consideredto be a polymicrobial disorder that is characterized by depletion ofvaginal Lactobacillus species that produce hydrogen peroxide and anincrease in the quantity of several vaginal anaerobic bacteria. See,e.g., Eschenbach et al., J. Clin. Microbiol. 27:251-256, 1989; Fredrickset al., J. Clin. Microbiol. 47:721-726, 2009.

The more recent use of cultivation-independent analyses of 16S rRNA genesequences has identified various, previously unrecognized species thatare prevalent in the vaginal flora and appear to be associated with BV.See, e.g., Fredricks et al., N. Engl. J. Med. 353:1899-1911, 2005;Ferris et al., J. Clin. Microbiol. 45:1016-1018, 2007. Among these arespecies most closely related to Megasphaera. See, e.g., Fredricks etal., supra. Recent studies also suggest that Megasphaera-like bacteriaplay an important role in BV pathogenesis and may be suitable markers ofdisease and treatment response. See Fredricks et al., J. Clin.Microbiol. 47:721-726, 2009.

Accordingly, there is a need for compositions, kits, and methods forrapidly and accurately detecting the presence or abundance ofMegasphaera in a specimen. Such compositions, kits, and methods would beparticularly useful for the diagnosis of BV or for monitoring apatient's response to BV treatment. The present invention meets theseand other needs.

SUMMARY

In one aspect, the present invention provides a combination of at leasttwo oligomers for detecting in a sample a Megasphaera sp. 16S rRNA or agene encoding a Megasphaera sp.16S rRNA. In some embodiments, for afirst Megasphaera target region, the oligomer combination comprises afirst amplification oligomer comprising a first target-hybridizingsequence that is from about 15 to about 25 contiguous nucleotidescontained in the sequence of SEQ ID NO:34 and that includes at least thesequence of SEQ ID NO:28; and a second amplification oligomer comprisinga second target-hybridizing sequence that is from about 15 to about 25contiguous nucleotides contained in the sequence of SEQ ID NO:36 andthat includes at least the sequence of SEQ ID NO:35. In otherembodiments, for a second Megasphaera target region, the oligomercombination comprises a first amplification oligomer comprising a firsttarget-hybridizing sequence that is from about 15 to about 25 contiguousnucleotides contained in the sequence of SEQ ID NO:38 and that includesat least the sequence of SEQ ID NO:37; and a second amplificationoligomer comprising a second target-hybridizing that is from about 15 toabout 25 contiguous nucleotides contained in the sequence of SEQ IDNO:40 and that includes at least the sequence of SEQ ID NO:39.

In certain embodiments of the oligomer combination for the firstMegasphaera target region, the first target-hybridizing sequence iscontained in the sequence of SEQ ID NO:29 and/or the secondtarget-hybridizing sequence is contained in the sequence of SEQ IDNO:33. The second target-hybridizing sequence may include at least thesequence of SEQ ID NO:32. Particularly suitable target-hybridizingsequences include SEQ ID NO:13 and SEQ ID NO:14 for the firstamplification oligomer and SEQ ID NO:19 and SEQ ID NO:20 for the secondamplification oligomer.

In certain embodiments of the oligomer combination for the secondMegasphaera target region, the first target-hybridizing sequence has thesequence shown in SEQ ID NO:15 and/or the second target hybridizingsequence has the sequence shown in SEQ ID NO:21.

In some variations, the second amplification oligomer is a promoterprimer further comprising a promoter sequence located 5′ to thetarget-hybridizing sequence. Suitable promoter sequences include T7 RNApolymerase promoter sequences such as, e.g., the sequence shown in SEQID NO:22. In more specific embodiments, for the first Megasphaera targetregion, the second amplification oligomer has the sequence shown in SEQID NO:16 or SEQ ID NO:17; or for the second Megasphaera target region,the second amplification oligomer has the sequence shown in SEQ IDNO:18.

An oligomer combination may further include at least one capture probeoligomer. In some such embodiments, the capture probe oligomer includesa target-hybridizing sequence covalently attached to a sequence ormoiety that binds to an immobilized probe. Suitable target-hybridizingsequences include the sequences shown in SEQ ID NOs:7-12. In particularvariations, the capture probe oligomer has a sequence selected from SEQID NOs:1-6.

An oligomer combination may also include at least one detection probeoligomer. In certain embodiments for the first Megasphaera targetregion, the detection probe oligomer includes a target-hybridizingsequence that is from about 14 to about 40 nucleotides in length and isconfigured to specifically hybridize to a target sequence containedwithin SEQ ID NO:45 from about nucleotide position 290 to aboutnucleotide position 334. In some such embodiments, the detection probetarget-hybridizing sequence is contained in the sequence of SEQ ID NO:31and includes at least the sequence of SEQ ID NO:30. In specificvariations, the detection probe target-hybridizing sequence for thefirst Megasphaera target region is selected from SEQ ID NO:23 and SEQ IDNO:25.

In certain embodiments comprising a detection probe oligomer for thesecond Megasphaera target region, the detection probe oligomer includesa target-hybridizing sequence that is from about 14 to about 40nucleotides in length and is configured to specifically hybridize to atarget sequence contained within SEQ ID NO:45 from about nucleotideposition 466 to about nucleotide position 536 or 607. In some suchembodiments, the detection probe target-hybridizing sequence iscontained in the sequence of SEQ ID NO:24 and includes at least thesequence of SEQ ID NO:26. In specific variations, the detection probetarget-hybridizing sequence for the second Megasphaera target region isselected from SEQ ID NO:24 and SEQ ID NO:26.

In yet other embodiments, an oligomer combination further comprises apseudotarget oligomer that can be amplified using the first and secondamplification oligomers. For example, in some variations for the firstMegasphaera target region, the pseudotarget has the sequence shown inSEQ ID NO:27. In other variations for the second Megasphaera targetregion, the pseudotarget oligomer has the sequence shown in SEQ IDNO:41, SEQ ID NO:42, SEQ ID NO:43, or SEQ ID NO:44.

In others aspects, the present invention provides a kit or a reactionmixture comprising the combination of at least two oligomers as above.

In yet another aspect, the present invention provides a method fordetecting, in a sample, a Megasphaera sp. target nucleic acid, whereinthe target nucleic acid is a Megasphaera sp. 16S rRNA or a gene encodingthe 16S rRNA. The method generally includes the following steps:

-   -   (a) providing a sample suspected of containing a Megasphaera sp.        bacterium;    -   (b) contacting the sample with at least two oligomers for        amplifying a Megasphaera sp. nucleic acid target region        corresponding to the target nucleic acid, the oligomer        combination comprising (i) for a first Megasphaera target        region, a first amplification oligomer comprising a first        target-hybridizing sequence that is from about 15 to about 25        contiguous nucleotides contained in the sequence of SEQ ID NO:34        and that includes at least the sequence of SEQ ID NO:28, and a        second amplification oligomer comprising a second        target-hybridizing sequence that is from about 15 to about 25        contiguous nucleotides contained in the sequence of SEQ ID NO:36        and that includes at least the sequence of SEQ ID NO:35; or (ii)        for a second Megasphaera target region, a first amplification        oligomer comprising a first target-hybridizing sequence that is        from about 15 to about 25 contiguous nucleotides contained in        the sequence of SEQ ID NO:38 and that includes at least the        sequence of SEQ ID NO:37, and a second amplification oligomer        comprising a second target-hybridizing that is from about 15 to        about 25 contiguous nucleotides contained in the sequence of SEQ        ID NO:40 and that includes at least the sequence of SEQ ID        NO:39;    -   (c) performing an in vitro nucleic acid amplification reaction,        where any Megasphaera target nucleic acid present in the sample        is used as a template for generating an amplification product;        and    -   (d) detecting the presence or absence of the amplification        product, thereby indicating the presence or absence of        Megasphaera sp. in said sample.

In certain embodiments of the method for the first Megasphaera targetregion, the first target-hybridizing sequence is contained in thesequence of SEQ ID NO:29 and/or the second target-hybridizing sequenceis contained in the sequence of SEQ ID NO:33. The secondtarget-hybridizing sequence may include at least the sequence of SEQ IDNO:32. Particularly suitable target-hybridizing sequences include SEQ IDNO:13 and SEQ ID NO:14 for the first amplification oligomer and SEQ IDNO:19 and SEQ ID NO:20 for the second amplification oligomer.

In certain embodiments of the method for the second Megasphaera targetregion, the first target-hybridizing sequence has the sequence shown inSEQ ID NO:15 and/or the second target hybridizing sequence has thesequence shown in SEQ ID NO:21.

In some variations of the method, the second amplification oligomer is apromoter primer further comprising a promoter sequence located 5′ to thetarget-hybridizing sequence. Suitable promoter sequences include T7 RNApolymerase promoter sequences such as, e.g., the sequence shown in SEQID NO:22. In more specific embodiments, for the first Megasphaera targetregion, the second amplification oligomer has the sequence shown in SEQID NO:16 or SEQ ID NO:17; or for the second Megasphaera target region,the second amplification oligomer has the sequence shown in SEQ IDNO:18.

Typically, the method for detecting the Megasphaera target nucleic acidfurther comprising purifying the Megasphaera target nucleic acid fromother components in the sample before the amplification step (b). Inparticular embodiments, the purifying step includes contacting thesample with at least one capture probe oligomer comprising atarget-hybridizing sequence covalently attached to a sequence or moietythat binds to an immobilized probe. Suitable target-hybridizingsequences include the sequences shown in SEQ ID NOs:7-12. In particularvariations, the capture probe oligomer has a sequence selected from SEQID NOs:1-6.

In some embodiments, the detecting step (d) includes contacting the invitro nucleic acid amplification reaction with a detection probeoligomer configured to specifically hybridize to the amplificationproduct under conditions whereby the presence or absence of theamplification product is determined, thereby indicating the presence orabsence of Megasphaera sp. in the sample. In particular embodiments forthe first Megasphaera target region, the detection probe oligomerincludes a target-hybridizing sequence that is from about 14 to about 40nucleotides in length and is configured to specifically hybridize to atarget sequence contained within SEQ ID NO:45 from about nucleotideposition 290 to about nucleotide position 334. In some such embodiments,the detection probe target-hybridizing sequence is contained in thesequence of SEQ ID NO:31 and includes at least the sequence of SEQ IDNO:30. In specific variations, the detection probe target-hybridizingsequence for the first Megasphaera target region is selected from SEQ IDNO:23 and SEQ ID NO:25.

In particular embodiments comprising use of a detection probe oligomerfor the second Megasphaera target region, the detection probe oligomerincludes a target-hybridizing sequence that is from about 14 to about 40nucleotides in length and is configured to specifically hybridize to atarget sequence contained within SEQ ID NO:45 from about nucleotideposition 466 to about nucleotide position 536 or 607. In some suchembodiments, the detection probe target-hybridizing sequence iscontained in the sequence of SEQ ID NO:24 and includes at least thesequence of SEQ ID NO:26. In specific variations, the detection probetarget-hybridizing sequence for the second Megasphaera target region isselected from SEQ ID NO:24 and SEQ ID NO:26.

In some embodiments of a method utilizing a detection probe oligomer,the detection probe includes at least one label. In specific variations,the one or more label(s) are selected from a chemiluminescent label, afluorescent label, a quencher, or any combination thereof.

In other embodiments of a method utilizing a detection probe oligomer,the detecting step (d) occurs during the amplifying step (c). In somesuch embodiments, the detection probe comprises a fluorescent label, aquencher, or both (e.g., a TaqMan detection probe or a molecularbeacon).

In still other embodiments of a method utilizing a detection probeoligomer, the detection probe further comprises a non-target-hybridizingsequence. In particular variations, the detection probe comprising anon-target-hybridizing sequence is a hairpin detection probe such as,e.g., a molecular beacon or a molecular torch.

In certain embodiments of the method for detecting the Megasphaeratarget nucleic acid, the amplification reaction at step (c) is anisothermal amplification reaction or a PCR amplification reaction. Inspecific variations, the amplification reaction is a real-timeamplification reaction.

In yet other embodiments, the method for detecting the Megasphaeratarget nucleic acid further includes contacting the sample with apseudotarget oligomer that can be amplified, using the first and secondamplification oligomers, in the in vitro nucleic acid amplificationreaction to generate a second amplification product that does notspecifically hybridize to the detection probe under the detectionreaction conditions. In some variations for the first Megasphaera targetregion, the pseudotarget has the sequence shown in SEQ ID NO:27. Inother variations for the second Megasphaera target region, thepseudotarget oligomer has the sequence shown in SEQ ID NO:41, SEQ IDNO:42, SEQ ID NO:43, or SEQ ID NO:44.

In still another aspect, the present invention provides a detectionprobe oligomer for detecting a Megasphaera sp. target nucleic acid. Insome embodiments, the detection probe oligomer comprises atarget-hybridizing sequence that is from about 14 to about 40nucleotides in length and is configured to specifically hybridize to atarget sequence contained within SEQ ID NO:45 from about nucleotideposition 290 to about nucleotide position 334. In some such embodiments,the detection probe target-hybridizing sequence is contained in thesequence of SEQ ID NO:31 and includes at least the sequence of SEQ IDNO:30. In specific variations, the detection probe target-hybridizingsequence for the first Megasphaera target region is selected from SEQ IDNO:23 and SEQ ID NO:25.

In other embodiments, a detection probe oligomer for detecting aMegasphaera sp. target nucleic acid comprises a target-hybridizingsequence that is from about 14 to about 40 nucleotides in length and isconfigured to specifically hybridize to a target sequence containedwithin SEQ ID NO:45 from about nucleotide position 466 to aboutnucleotide position 536 or 607. In some such embodiments, the detectionprobe target-hybridizing sequence is contained in the sequence of SEQ IDNO:24 and includes at least the sequence of SEQ ID NO:26. In specificvariations, the detection probe target-hybridizing sequence for thesecond Megasphaera target region is selected from SEQ ID NO:24 and SEQID NO:26.

In some embodiments of a detection probe oligomer, the detection probeincludes at least one label. In specific variations, the one or morelabel(s) are selected from a chemiluminescent label, a fluorescentlabel, a quencher, or any combination thereof. In more specificvariations the detection probe comprises a fluorescent label and aquencher (e.g., a TaqMan detection probe or a molecular beacon).

In other embodiments of a detection probe oligomer, the detection probefurther comprises a non-target-hybridizing sequence. In particularvariations, the detection probe comprising a non-target-hybridizingsequence is a hairpin detection probe such as, e.g., a molecular beaconor a molecular torch.

These and other aspects of the invention will become evident uponreference to the following detailed description of the invention and theattached drawings.

DEFINITIONS

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art pertinent to the methods and compositions described. As usedherein, the following terms and phrases have the meanings ascribed tothem unless specified otherwise.

The terms “a,” “an,” and “the” include plural referents, unless thecontext clearly indicates otherwise. For example, “a nucleic acid” asused herein is understood to represent one or more nucleic acids. Assuch, the terms “a” (or “an”), “one or more,” and “at least one” can beused interchangeably herein.

“Sample” includes any specimen that may contain Megasphaera sp. (e.g.,Megasphaera elsdenii) or components thereof, such as nucleic acids orfragments of nucleic acids. Samples include “biological samples” whichinclude any tissue or material derived from a living or dead human thatmay contain Megasphaera sp. or target nucleic acid derived therefrom,including, e.g., vaginal swab samples, cervical brush samples,respiratory tissue or exudates such as bronchoscopy, bronchoalveolarlavage (BAL) or lung biopsy, sputum, saliva, peripheral blood, plasma,serum, lymph node, gastrointestinal tissue, feces, urine, semen or otherbody fluids or materials. The biological sample may be treated tophysically or mechanically disrupt tissue or cell structure, thusreleasing intracellular components into a solution which may furthercontain enzymes, buffers, salts, detergents and the like, which are usedto prepare, using standard methods, a biological sample for analysis.Also, samples may include processed samples, such as those obtained frompassing samples over or through a filtering device, or followingcentrifugation, or by adherence to a medium, matrix, or support.

“Nucleic acid” refers to a multimeric compound comprising two or morecovalently bonded nucleosides or nucleoside analogs having nitrogenousheterocyclic bases, or base analogs, where the nucleosides are linkedtogether by phosphodiester bonds or other linkages to form apolynucleotide. Nucleic acids include RNA, DNA, or chimeric DNA-RNApolymers or oligonucleotides, and analogs thereof. A nucleic acid“backbone” may be made up of a variety of linkages, including one ormore of sugar-phosphodiester linkages, peptide-nucleic acid bonds (in“peptide nucleic acids” or PNAs, see, e.g., International PatentApplication Pub. No. WO 95/32305), phosphorothioate linkages,methylphosphonate linkages, or combinations thereof. Sugar moieties ofthe nucleic acid may be either ribose or deoxyribose, or similarcompounds having known substitutions such as, for example, 2′-methoxysubstitutions and 2′-halide substitutions (e.g., 2′ -F). Nitrogenousbases may be conventional bases (A, G, C, T, U), analogs thereof (e.g.,inosine, 5-methylisocytosine, isoguanine; see, e.g., The Biochemistry ofthe Nucleic Acids 5-36, Adams et al., ed., 11th ed., 1992; Abraham etal., 2007, BioTechniques 43: 617-24), which include derivatives ofpurine or pyrimidine bases (e.g., N⁴-methyl deoxygaunosine, deaza- oraza-purines, deaza- or aza-pyrimidines, pyrimidine bases havingsubstituent groups at the 5 or 6 position, purine bases having analtered or replacement substituent at the 2, 6 and/or 8 position, suchas 2-amino-6-methylaminopurine, O⁶-methylguanine, 4-thio-pyrimidines,4-amino-pyrimidines, 4-dimethylhydrazine- pyrimidines, andO⁴-alkyl-pyrimidines, and pyrazolo-compounds, such as unsubstituted or3-substituted pyrazolo[3,4-d]pyrimidine; U.S. Pat. Nos. 5,378,825,6,949,367 and International Patent Application Pub. No. WO93/13121, eachincorporated by reference herein). Nucleic acids may include “abasic”residues in which the backbone does not include a nitrogenous base forone or more residues (see, e.g., U.S. Pat. No. 5,585,481, incorporatedby reference herein). A nucleic acid may comprise only conventionalsugars, bases, and linkages as found in RNA and DNA, or may includeconventional components and substitutions (e.g., conventional baseslinked by a 2′ -methoxy backbone, or a nucleic acid including a mixtureof conventional bases and one or more base analogs). Nucleic acids mayinclude “locked nucleic acids” (LNA), in which one or more nucleotidemonomers have a bicyclic furanose unit locked in an RNA mimicking sugarconformation, which enhances hybridization affinity toward complementarysequences in single-stranded RNA (ssRNA), single-stranded DNA (ssDNA),or double-stranded DNA (dsDNA) (Venter et al., Biochemistry 43:13233-41,2004, incorporated by reference herein). Nucleic acids may includemodified bases to alter the function or behavior of the nucleic acid,e.g., addition of a 3′-terminal dideoxynucleotide to block additionalnucleotides from being added to the nucleic acid. Synthetic methods formaking nucleic acids in vitro are well known in the art although nucleicacids may be purified from natural sources using routine techniques.

The term “polynucleotide” as used herein denotes a nucleic acid chain.Throughout this application, nucleic acids are designated by the5′-terminus to the 3′-terminus. Standard nucleic acids, e.g., DNA andRNA, are typically synthesized “3′-to-5′,” i.e., by the addition ofnucleotides to the 5′-terminus of a growing nucleic acid.

A “nucleotide” as used herein is a subunit of a nucleic acid consistingof a phosphate group, a 5-carbon sugar and a nitrogenous base. The5-carbon sugar found in RNA is ribose. In DNA, the 5-carbon sugar is2′-deoxyribose. The term also includes analogs of such subunits, such asa methoxy group at the 2′ position of the ribose (2′-O-Me). As usedherein, methoxy oligonucleotides containing “T” residues have a methoxygroup at the 2′ position of the ribose moiety, and a uracil at the baseposition of the nucleotide.

A “non-nucleotide unit” as used herein is a unit that does notsignificantly participate in hybridization of a polymer. Such units mustnot, for example, participate in any significant hydrogen bonding with anucleotide, and would exclude units having as a component one of thefive nucleotide bases or analogs thereof.

A “target nucleic acid” as used herein is a nucleic acid comprising atarget sequence to be amplified. Target nucleic acids may be DNA or RNAas described herein, and may be either single-stranded ordouble-stranded. The target nucleic acid may include other sequencesbesides the target sequence, which may not be amplified. Typical targetnucleic acids include virus genomes, bacterial genomes, fungal genomes,plant genomes, animal genomes, rRNA, tRNA, or mRNA from viruses,bacteria or eukaryotic cells, mitochondrial DNA, or chromosomal DNA.

By “isolated” it is meant that a sample containing a target nucleic acidis taken from its natural milieu, but the term does not connote anydegree of purification.

The term “target sequence” as used herein refers to the particularnucleotide sequence of the target nucleic acid that is to be amplifiedand/or detected. The “target sequence” includes the complexing sequencesto which oligonucleotides (e.g., priming oligonucleotides and/orpromoter oligonucleotides) complex during an amplification processes(e.g., TMA). Where the target nucleic acid is originallysingle-stranded, the term “target sequence” will also refer to thesequence complementary to the “target sequence” as present in the targetnucleic acid. Where the target nucleic acid is originallydouble-stranded, the term “target sequence” refers to both the sense (+)and antisense (−) strands. In choosing a target sequence, the skilledartisan will understand that a “unique” sequence should be chosen so asto distinguish between unrelated or closely related target nucleicacids.

“Target-hybridizing sequence” is used herein to refer to the portion ofan oligomer that is configured to hybridize with a target nucleic acidsequence. Preferably, the target-hybridizing sequences are configured tospecifically hybridize with a target nucleic acid sequence.Target-hybridizing sequences may be 100% complementary to the portion ofthe target sequence to which they are configured to hybridize; but notnecessarily. Target-hybridizing sequences may also include inserted,deleted and/or substituted nucleotide residues relative to a targetsequence. Less than 100% complementarity of a target-hybridizingsequence to a target sequence may arise, for example, when the targetnucleic acid is a plurality strains within a species, such as would bethe case for an oligomer configured to hybridize to the various strainsof Megasphaera. It is understood that other reasons exist forconfiguring a target-hybridizing sequence to have less than 100%complementarity to a target nucleic acid.

Oligomer target-hybridizing sequences defined herein by reference to aspecific sequence (e.g., by reference a region within SEQ ID NO:45) arealso understood to include functional complements thereof, unless thecontext clearly dictates otherwise. Thus, for example, wheretarget-hybridizing regions of first and second amplification oligomersare defined by reference to specific sequences corresponding,respectively, to sense and antisense strands of a target nucleic acid,it is understood that the amplification oligomer combination may includea functional combination of first and second amplification oligomershaving target-hybridizing sequences that are the respective complementsof the specific reference sequences. Similarly, and again by way ofexample, where a target-hybridizing sequence for a detection probeoligomer is defined reference to a specific sequence, it is understoodthat the detection probe may include a corresponding detection probeoligomer having a target-hybridizing sequence that is the complement ofthe specific reference sequence; or where a detection probe oligomer isdefined by its configuration to hybridize to a specific sequence, it isunderstood that the detection probe may include a correspondingdetection probe oligomer having a target-hybridizing sequence that isconfigured to hybridize to the complement of the specific referencesequence.

The term “targets a sequence” as used herein in reference to a region ofMegasphaera nucleic acid refers to a process whereby an oligonucleotidehybridizes to the target sequence in a manner that allows foramplification and detection as described herein. In one preferredembodiment, the oligonucleotide is complementary with the targetedMegasphaera nucleic acid sequence and contains no mismatches. In anotherpreferred embodiment, the oligonucleotide is complementary but contains1, 2, 3, 4, or 5 mismatches with the targeted Megasphaera nucleic acidsequence. Preferably, the oligonucleotide that hybridizes to theMegasphaera nucleic acid sequence includes at least 10 to as many as 50nucleotides complementary to the target sequence. It is understood thatat least 10 and as many as 50 is an inclusive range such that 10, 50 andeach whole number there between are included. Preferably, the oligomerspecifically hybridizes to the target sequence.

The term “configured to” denotes an actual arrangement of thepolynucleotide sequence configuration of a referenced oligonucleotidetarget-hybridizing sequence. For example, amplification oligomers thatare configured to generate a specified amplicon from a target sequencehave polynucleotide sequences that hybridize to the target sequence andcan be used in an amplification reaction to generate the amplicon. Alsoas an example, oligonucleotides that are configured to specificallyhybridize to a target sequence have a polynucleotide sequence thatspecifically hybridizes to the referenced sequence under stringenthybridization conditions.

The term “configured to specifically hybridize to” as used herein meansthat the target- hybridizing region of an amplification oligonucleotide,detection probe, or other oligonucleotide is designed to have apolynucleotide sequence that could target a sequence of the referencedMegasphaera target region. Such an oligonucleotide is not limited totargeting that sequence only, but is rather useful as a composition, ina kit or in a method for targeting a Megasphaera target nucleic acid.The oligonucleotide is designed to function as a component of an assayfor amplification and detection of Megasphaera from a sample, andtherefore is designed to target Megasphaera in the presence of othernucleic acids commonly found in testing samples. “Specifically hybridizeto” does not mean exclusively hybridize to, as some small level ofhybridization to non-target nucleic acids may occur, as is understood inthe art. Rather, “specifically hybridize to” means that theoligonucleotide is configured to function in an assay to primarilyhybridize the target so that an accurate detection of target nucleicacid in a sample can be determined. The term “configured to” denotes anactual arrangement of the polynucleotide sequence configuration of theamplification oligonucleotide target-hybridizing sequence.

The term “fragment,” as used herein in reference to the Megasphaeratargeted nucleic acid, refers to a piece of contiguous nucleic acid. Incertain embodiments, the fragment includes contiguous nucleotides from aMegasphaera 16S ribosomal RNA, wherein the number of 16S contiguousnucleotides in the fragment are less than that for the entire 16S.

The term “region,” as used herein, refers to a portion of a nucleic acidwherein said portion is smaller than the entire nucleic acid. Forexample, when the nucleic acid in reference is an oligonucleotidepromoter primer, the term “region” may be used refer to the smallerpromoter portion of the entire oligonucleotide. Similarly, and also asexample only, when the nucleic acid is a 16S ribosomal RNA, the term“region” may be used to refer to a smaller area of the nucleic acid,wherein the smaller area is targeted by one or more oligonucleotides ofthe invention. As another non-limiting example, when the nucleic acid inreference is an amplicon, the term region may be used to refer to thesmaller nucleotide sequence identified for hybridization by thetarget-hybridizing sequence of a probe.

The interchangeable terms “oligomer,” “oligo,” and “oligonucleotide”refer to a nucleic acid having generally less than 1,000 nucleotide (nt)residues, including polymers in a range having a lower limit of about 5nt residues and an upper limit of about 500 to 900 nt residues. In someembodiments, oligonucleotides are in a size range having a lower limitof about 12 to 15 nt and an upper limit of about 50 to 600 nt, and otherembodiments are in a range having a lower limit of about 15 to 20 nt andan upper limit of about 22 to 100 nt. Oligonucleotides may be purifiedfrom naturally occurring sources or may be synthesized using any of avariety of well-known enzymatic or chemical methods. The termoligonucleotide does not denote any particular function to the reagent;rather, it is used generically to cover all such reagents describedherein. An oligonucleotide may serve various different functions. Forexample, it may function as a primer if it is specific for and capableof hybridizing to a complementary strand and can further be extended inthe presence of a nucleic acid polymerase; it may function as a primerand provide a promoter if it contains a sequence recognized by an RNApolymerase and allows for transcription (e.g., a T7 Primer); and it mayfunction to detect a target nucleic acid if it is capable of hybridizingto the target nucleic acid, or an amplicon thereof, and further providesa detectible moiety (e.g., an acridinium-ester compound).

As used herein, an oligonucleotide “substantially corresponding to” aspecified reference nucleic acid sequence means that the oligonucleotideis sufficiently similar to the reference nucleic acid sequence such thatthe oligonucleotide has similar hybridization properties to thereference nucleic acid sequence in that it would hybridize with the sametarget nucleic acid sequence under stringent hybridization conditions.One skilled in the art will understand that “substantially correspondingoligonucleotides” can vary from a reference sequence and still hybridizeto the same target nucleic acid sequence. It is also understood that afirst nucleic acid corresponding to a second nucleic acid includes theRNA and DNA thereof and includes the complements thereof, unless thecontext clearly dictates otherwise. This variation from the nucleic acidmay be stated in terms of a percentage of identical bases within thesequence or the percentage of perfectly complementary bases between theprobe or primer and its target sequence. Thus, in certain embodiments,an oligonucleotide “substantially corresponds” to a reference nucleicacid sequence if these percentages of base identity or complementarityare from 100% to about 80%. In preferred embodiments, the percentage isfrom 100% to about 85%. In more preferred embodiments, this percentageis from 100% to about 90%; in other preferred embodiments, thispercentage is from 100% to about 95%. Similarly, a region of a nucleicacid or amplified nucleic acid can be referred to herein ascorresponding to a reference nucleic acid sequence. One skilled in theart will understand the various modifications to the hybridizationconditions that might be required at various percentages ofcomplementarity to allow hybridization to a specific target sequencewithout causing an unacceptable level of non-specific hybridization.

A “helper oligonucleotide” or “helper” refers to an oligonucleotidedesigned to bind to a target nucleic acid and impose a differentsecondary and/or tertiary structure on the target to increase the rateand extent of hybridization of a detection probe or otheroligonucleotide with the targeted nucleic acid, as described, forexample, in U.S. Pat. No. 5,030,557, incorporated by reference herein.Helpers may also be used to assist with the target hybridization andfunction of primer, target capture and other oligonucleotides.

As used herein, a “blocking moiety” is a substance used to “block” the3′-terminus of an oligonucleotide or other nucleic acid so that itcannot be efficiently extended by a nucleic acid polymerase. Oligomersnot intended for extension by a nucleic acid polymerase may include ablocker group that replaces the 3′OH to prevent enzyme-mediatedextension of the oligomer in an amplification reaction. For example,blocked amplification oligomers and/or detection probes present duringamplification may not have functional 3′OH and instead include one ormore blocking groups located at or near the 3′ end. In some embodimentsa blocking group near the 3′ end and may be within five residues of the3′ end and is sufficiently large to limit binding of a polymerase to theoligomer. In other embodiments a blocking group is covalently attachedto the 3′ terminus. Many different chemical groups may be used to blockthe 3′ end, e.g., alkyl groups, non-nucleotide linkers, alkane-dioldideoxynucleotide residues, and cordycepin.

An “amplification oligomer” is an oligomer, at least the 3′ -end ofwhich is complementary to a target nucleic acid, and which hybridizes toa target nucleic acid, or its complement, and participates in a nucleicacid amplification reaction. An example of an amplification oligomer isa “primer” that hybridizes to a target nucleic acid and contains a 3′ OHend that is extended by a polymerase in an amplification process.Another example of an amplification oligomer is an oligomer that is notextended by a polymerase (e.g., because it has a 3′ blocked end) butparticipates in or facilitates amplification. For example, the 5′ regionof an amplification oligonucleotide may include a promoter sequence thatis non-complementary to the target nucleic acid (which may be referredto as a “promoter primer” or “promoter provider”). Those skilled in theart will understand that an amplification oligomer that functions as aprimer may be modified to include a 5′ promoter sequence, and thusfunction as a promoter primer. Incorporating a 3′ blocked end furthermodifies the promoter primer, which is now capable of hybridizing to atarget nucleic acid and providing an upstream promoter sequence thatserves to initiate transcription, but does not provide a primer foroligo extension. Such a modified oligo is referred to herein as a“promoter provider” oligomer. Size ranges for amplificationoligonucleotides include those that are about 10 to about 70 nt long(not including any promoter sequence or poly-A tails) and contain atleast about 10 contiguous bases, or even at least 12 contiguous basesthat are complementary to a region of the target nucleic acid sequence(or a complementary strand thereof). The contiguous bases are at least80%, or at least 90%, or completely complementary to the target sequenceto which the amplification oligomer binds. An amplification oligomer mayoptionally include modified nucleotides or analogs, or additionalnucleotides that participate in an amplification reaction but are notcomplementary to or contained in the target nucleic acid, or templatesequence. It is understood that when referring to ranges for the lengthof an oligonucleotide, amplicon, or other nucleic acid, that the rangeis inclusive of all whole numbers (e.g., 19-25 contiguous nucleotides inlength includes 19, 20, 21, 22, 23, 24 & 25).

As used herein, a “promoter” is a specific nucleic acid sequence that isrecognized by a DNA-dependent RNA polymerase (“transcriptase”) as asignal to bind to the nucleic acid and begin the transcription of RNA ata specific site.

As used herein, a “promoter provider” or “provider” refers to anoligonucleotide comprising first and second regions, and which ismodified to prevent the initiation of DNA synthesis from its 3′-terminus. The “first region” of a promoter provider oligonucleotidecomprises a base sequence which hybridizes to a DNA template, where thehybridizing sequence is situated 3′, but not necessarily adjacent to, apromoter region. The hybridizing portion of a promoter oligonucleotideis typically at least 10 nucleotides in length, and may extend up to 50or more nucleotides in length. The “second region” comprises a promotersequence for an RNA polymerase. A promoter oligonucleotide is engineeredso that it is incapable of being extended by an RNA- or DNA-dependentDNA polymerase, e.g., reverse transcriptase, preferably comprising ablocking moiety at its 3′-terminus as described above. As referred toherein, a “T7 Provider” is a blocked promoter provider oligonucleotidethat provides an oligonucleotide sequence that is recognized by T7 RNApolymerase.

As used herein, a “terminating oligonucleotide” or “blockeroligonucleotide” is an oligonucleotide comprising a base sequence thatis complementary to a region of the target nucleic acid in the vicinityof the 5′ -end of the target sequence, so as to “terminate” primerextension of a nascent nucleic acid that includes a primingoligonucleotide, thereby providing a defined 3′-end for the nascentnucleic acid strand.

An “extender oligomer” or “extend oligomer” as used herein refers to anoligonucleotide that is the same sense as the T7 Provider and may act asa helper oligonucleotide that opens up structure or improvesspecificity.

“Amplification” refers to any known procedure for obtaining multiplecopies of a target nucleic acid sequence or its complement or fragmentsthereof. The multiple copies may be referred to as amplicons oramplification products. Amplification of “fragments” refers toproduction of an amplified nucleic acid that contains less than thecomplete target nucleic acid or its complement, e.g., produced by usingan amplification oligonucleotide that hybridizes to, and initiatespolymerization from, an internal position of the target nucleic acid.Known amplification methods include, for example, replicase-mediatedamplification, polymerase chain reaction (PCR), ligase chain reaction(LCR), strand-displacement amplification (SDA), andtranscription-mediated or transcription-associated amplification.Replicase-mediated amplification uses self-replicating RNA molecules,and a replicase such as QB-replicase (see, e.g., U.S. Pat. No.4,786,600, incorporated by reference herein). PCR amplification uses aDNA polymerase, pairs of primers, and thermal cycling to synthesizemultiple copies of two complementary strands of dsDNA or from a cDNA(see, e.g., U.S. Pat. Nos. 4,683,195; 4,683,202; and 4,800,159; eachincorporated by reference herein). LCR amplification uses four or moredifferent oligonucleotides to amplify a target and its complementarystrand by using multiple cycles of hybridization, ligation, anddenaturation (see, e.g., U.S. Pat. Nos. 5,427,930 and 5,516,663, eachincorporated by reference herein). SDA uses a primer that contains arecognition site for a restriction endonuclease and an endonuclease thatnicks one strand of a hemimodified DNA duplex that includes the targetsequence, whereby amplification occurs in a series of primer extensionand strand displacement steps (see, e.g., U.S. Pat. Nos. 5,422,252;5,547,861; and 5,648,211; each incorporated by reference herein).

“Transcription-associated amplification” or “transcription-mediatedamplification” (TMA) refer to nucleic acid amplification that uses anRNA polymerase to produce multiple RNA transcripts from a nucleic acidtemplate. These methods generally employ an RNA polymerase, a DNApolymerase, deoxyribonucleoside triphosphates, ribonucleosidetriphosphates, and a template complementary oligonucleotide thatincludes a promoter sequence, and optionally may include one or moreother oligonucleotides. TMA methods and single-primer transcriptionassociated amplification method are embodiments of amplification methodsused for detection of Megasphaera target sequences as described herein.Variations of transcription-associated amplification are well known inthe art as previously disclosed in detail (see, e.g., U.S. Pat. Nos.4,868,105; 5,124,246; 5,130,238; 5,399,491; 5,437,990; 5,554,516; and7,374,885; and International Patent Application Pub. Nos. WO 88/01302;WO 88/10315; and WO 95/03430; each incorporated by reference herein).The person of ordinary skill in the art will appreciate that thedisclosed compositions may be used in amplification methods based onextension of oligomer sequences by a polymerase.

As used herein, the term “real-time TMA” refers to single-primertranscription-mediated amplification (“TMA”) of target nucleic acid thatis monitored by real-time detection means.

The term “amplicon” or the term “amplification product” as used hereinrefers to the nucleic acid molecule generated during an amplificationprocedure that is complementary or homologous to a sequence containedwithin the target sequence. The complementary or homologous sequence ofan amplicon is sometimes referred to herein as a “target-specificsequence.” Amplicons generated using the amplification oligomers of thecurrent invention may comprise non-target specific sequences. Ampliconscan be double stranded or single stranded and can include DNA, RNA orboth. For example, DNA-dependent RNA polymerase transcribes singlestranded amplicons from double-stranded DNA duringtranscription-mediated amplification procedures. These single-strandedamplicons are RNA amplicons and can be either strand of adouble-stranded complex, depending on how the amplification oligomersare configured. Thus, amplicons can be single-stranded RNA.RNA-dependent DNA polymerases synthesize a DNA strand that iscomplementary to an RNA template. Thus, amplicons can be double-strandedDNA and RNA hybrids. RNA-dependent DNA polymerases often include RNaseactivity, or are used in conjunction with an RNase, which degrades theRNA strand. Thus, amplicons can be single stranded DNA. RNA-dependentDNA polymerases and DNA-dependent DNA polymerases synthesizecomplementary DNA strands from DNA templates. Thus, amplicons can bedouble-stranded DNA. RNA- dependent RNA polymerases synthesize RNA froman RNA template. Thus, amplicons can be double-stranded RNA.DNA-dependent RNA polymerases synthesize RNA from double-stranded DNAtemplates, also referred to as transcription. Thus, amplicons can besingle stranded RNA. Amplicons and methods for generating amplicons areknown to those skilled in the art. For convenience herein, a singlestrand of RNA or a single strand of DNA may represent an amplicongenerated by an amplification oligomer combination of the currentinvention. Such representation is not meant to limit the amplicon to therepresentation shown. Skilled artisans in possession of the instantdisclosure will use amplification oligomers and polymerase enzymes togenerate any of the numerous types of amplicons, all within the spiritand scope of the current invention.

A “non-target-specific sequence,” as is used herein refers to a regionof an oligomer sequence, wherein said region does not stably hybridizewith a target sequence under standard hybridization conditions.Oligomers with non-target-specific sequences include, but are notlimited to, promoter primers and molecular beacons. An amplificationoligomer may contain a sequence that is not complementary to the targetor template sequence; for example, the 5′ region of a primer may includea promoter sequence that is non-complementary to the target nucleic acid(referred to as a “promoter primer”). Those skilled in the art willunderstand that an amplification oligomer that functions as a primer maybe modified to include a 5′ promoter sequence, and thus function as apromoter primer. Similarly, a promoter primer may be modified by removalof, or synthesis without, a promoter sequence and still function as aprimer. A 3′ blocked amplification oligomer may provide a promotersequence and serve as a template for polymerization (referred to as a“promoter provider”). Thus, an amplicon that is generated by anamplification oligomer member such as a promoter primer will comprise atarget-specific sequence and a non-target-specific sequence.

“Detection probe,” “detection oligonucleotide,” and “detection probeoligomer” are used interchangeably to refer to a nucleic acid oligomerthat hybridizes specifically to a target sequence in a nucleic acid, orin an amplified nucleic acid, under conditions that promotehybridization to allow detection of the target sequence or amplifiednucleic acid. Detection may either be direct (e.g., a probe hybridizeddirectly to its target sequence) or indirect (e.g., a probe linked toits target via an intermediate molecular structure). Detection probesmay be DNA, RNA, analogs thereof or combinations thereof and they may belabeled or unlabeled. Detection probes may further include alternativebackbone linkages such as, e.g., 2′-O-methyl linkages. A detectionprobe's “target sequence” generally refers to a smaller nucleic acidsequence region within a larger nucleic acid sequence that hybridizesspecifically to at least a portion of a probe oligomer by standard basepairing. A detection probe may comprise target-specific sequences andother sequences that contribute to the three-dimensional conformation ofthe probe (see, e.g., U.S. Pat. Nos. 5,118,801; 5,312,728; 6,849,412;6,835,542; 6,534,274; and 6,361,945; and U.S. Patent Application Pub.No. 20060068417; each incorporated by reference herein).

By “stable” or “stable for detection” is meant that the temperature of areaction mixture is at least 2° C. below the melting temperature of anucleic acid duplex.

As used herein, a “label” refers to a moiety or compound joined directlyor indirectly to a probe that is detected or leads to a detectablesignal. Direct labeling can occur through bonds or interactions thatlink the label to the probe, including covalent bonds or non-covalentinteractions, e.g., hydrogen bonds, hydrophobic and ionic interactions,or formation of chelates or coordination complexes. Indirect labelingcan occur through use of a bridging moiety or “linker” such as a bindingpair member, an antibody or additional oligomer, which is eitherdirectly or indirectly labeled, and which may amplify the detectablesignal. Labels include any detectable moiety, such as a radionuclide,ligand (e.g., biotin, avidin), enzyme or enzyme substrate, reactivegroup, or chromophore (e.g., dye, particle, or bead that impartsdetectable color), luminescent compound (e.g., bioluminescent,phosphorescent, or chemiluminescent labels), or fluorophore. Labels maybe detectable in a homogeneous assay in which bound labeled probe in amixture exhibits a detectable change different from that of an unboundlabeled probe, e.g., instability or differential degradation properties.A “homogeneous detectable label” can be detected without physicallyremoving bound from unbound forms of the label or labeled probe (see,e.g., U.S. Pat. Nos. 5,283,174; 5,656,207; and 5,658,737; eachincorporated by reference herein). Labels include chemiluminescentcompounds, e.g., acridinium ester (“AE”) compounds that include standardAE and derivatives (see, e.g., U.S. Pat. Nos. 5,656,207; 5,658,737; and5,639,604; each incorporated by reference herein). Synthesis and methodsof attaching labels to nucleic acids and detecting labels are wellknown. (See, e.g., Sambrook et al., Molecular Cloning, A LaboratoryManual, 2nd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Habor,N.Y., 1989), Chapter 10, incorporated by reference herein. See also U.S.Pat. Nos. 5,658,737; 5,656,207; 5,547,842; 5,283,174; and 4,581,333;each incorporated by reference herein). More than one label, and morethan one type of label, may be present on a particular probe, ordetection may use a mixture of probes in which each probe is labeledwith a compound that produces a detectable signal (see, e.g., U.S. Pat.Nos. 6,180,340 and 6,350,579, each incorporated by reference herein).

“Capture probe,” “capture oligonucleotide,” and “capture probe oligomer”are used interchangeably to refer to a nucleic acid oligomer thatspecifically hybridizes to a target sequence in a target nucleic acid bystandard base pairing and joins to a binding partner on an immobilizedprobe to capture the target nucleic acid to a support. One example of acapture oligomer includes two binding regions: a sequence-binding region(e.g., target-specific portion) and an immobilized probe-binding region,usually on the same oligomer, although the two regions may be present ontwo different oligomers joined together by one or more linkers. Anotherembodiment of a capture oligomer uses a target-sequence binding regionthat includes random or non- random poly-GU, poly-GT, or poly Usequences to bind non-specifically to a target nucleic acid and link itto an immobilized probe on a support.

As used herein, an “immobilized oligonucleotide,” “immobilized probe,”or “immobilized nucleic acid” refers to a nucleic acid binding partnerthat joins a capture oligomer to a support, directly or indirectly. Animmobilized probe joined to a support facilitates separation of acapture probe bound target from unbound material in a sample. Oneembodiment of an immobilized probe is an oligomer joined to a supportthat facilitates separation of bound target sequence from unboundmaterial in a sample. Supports may include known materials, such asmatrices and particles free in solution, which may be made ofnitrocellulose, nylon, glass, polyacrylate, mixed polymers, polystyrene,silane, polypropylene, metal, or other compositions, of which oneembodiment is magnetically attractable particles. Supports may bemonodisperse magnetic spheres (e.g., uniform size ±5%), to which animmobilized probe is joined directly (via covalent linkage, chelation,or ionic interaction), or indirectly (via one or more linkers), wherethe linkage or interaction between the probe and support is stableduring hybridization conditions.

By “complementary” is meant that the nucleotide sequences of similarregions of two single-stranded nucleic acids, or to different regions ofthe same single-stranded nucleic acid have a nucleotide base compositionthat allow the single-stranded regions to hybridize together in a stabledouble-stranded hydrogen-bonded region under stringent hybridization oramplification conditions. Sequences that hybridize to each other may becompletely complementary or partially complementary to the intendedtarget sequence by standard nucleic acid base pairing (e.g., G:C, A:T orA:U pairing). By “sufficiently complementary” is meant a contiguoussequence that is capable of hybridizing to another sequence by hydrogenbonding between a series of complementary bases, which may becomplementary at each position in the sequence by standard base pairingor may contain one or more residues, including abasic residues, that arenot complementary. Sufficiently complementary contiguous sequencestypically are at least 80%, or at least 90%, complementary to a sequenceto which an oligomer is intended to specifically hybridize. Sequencesthat are “sufficiently complementary” allow stable hybridization of anucleic acid oligomer with its target sequence under appropriatehybridization conditions, even if the sequences are not completelycomplementary. When a contiguous sequence of nucleotides of onesingle-stranded region is able to form a series of “canonical”hydrogen-bonded base pairs with an analogous sequence of nucleotides ofthe other single-stranded region, such that A is paired with U or T andC is paired with G, the nucleotides sequences are “completely”complementary (see, e.g., Sambrook et al., Molecular Cloning, ALaboratory Manual, 2^(nd) ed. (Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., 1989) at §§1.90-1.91, 7.37-7.57, 9.47-9.51 and11.47-11.57, particularly §§9.50-9.51, 11.12-11.13, 11.45-11.47 and11.55-11.57, incorporated by reference herein). It is understood thatranges for percent identity are inclusive of all whole and partialnumbers (e.g., at least 90% includes 90, 91, 93.5, 97.687 and etc.).

By “preferentially hybridize” or “specifically hybridize” is meant thatunder stringent hybridization assay conditions, probes hybridize totheir target sequences, or replicates thereof, to form stableprobe:target hybrids, while at the same time formation of stableprobe:non-target hybrids is minimized. Thus, a probe hybridizes to atarget sequence or replicate thereof to a sufficiently greater extentthan to a non-target sequence, to enable one having ordinary skill inthe art to accurately quantitate the RNA replicates or complementary DNA(cDNA) of the target sequence formed during the amplification.Appropriate hybridization conditions are well-known in the art, may bepredicted based on sequence composition, or can be determined by usingroutine testing methods (see, e.g., Sambrook et al., Molecular Cloning,A Laboratory Manual, 2^(nd) ed. (Cold Spring Harbor Laboratory Press,Cold Spring Harbor, N.Y., 1989) at §§1.90-1.91, 7.37-7.57, 9.47-9.51 and11.47-11.57, particularly §§9.50-9.51, 11.12-11.13, 11.45-11.47 and11.55-11.57, incorporated by reference herein).

By “nucleic acid hybrid,” “hybrid,” or “duplex” is meant a nucleic acidstructure containing a double-stranded, hydrogen-bonded region whereineach strand is complementary to the other, and wherein the region issufficiently stable under stringent hybridization conditions to bedetected by means including, but not limited to, chemiluminescent orfluorescent light detection, autoradiography, or gel electrophoresis.Such hybrids may comprise RNA:RNA, RNA:DNA, or DNA:DNA duplex molecules.

“Sample preparation” refers to any steps or method that treats a samplefor subsequent amplification and/or detection of Megasphaera nucleicacids present in the sample. Samples may be complex mixtures ofcomponents of which the target nucleic acid is a minority component.Sample preparation may include any known method of concentratingcomponents, such as microbes or nucleic acids, from a larger samplevolume, such as by filtration of airborne or waterborne particles from alarger volume sample or by isolation of microbes from a sample by usingstandard microbiology methods. Sample preparation may include physicaldisruption and/or chemical lysis of cellular components to releaseintracellular components into a substantially aqueous or organic phaseand removal of debris, such as by using filtration, centrifugation oradsorption. Sample preparation may include use of a nucleic acidoligonucleotide that selectively or non-specifically capture a targetnucleic acid and separate it from other sample components (e.g., asdescribed in U.S. Pat. No. 6,110,678 and International PatentApplication Pub. No. WO 2008/016988, each incorporated by referenceherein).

“Separating” or “purifying” means that one or more components of asample are removed or separated from other sample components. Samplecomponents include target nucleic acids usually in a generally aqueoussolution phase, which may also include cellular fragments, proteins,carbohydrates, lipids, and other nucleic acids. Separating or purifyingremoves at least 70%, or at least 80%, or at least 95% of the targetnucleic acid from other sample components.

As used herein, a “DNA-dependent DNA polymerase” is an enzyme thatsynthesizes a complementary DNA copy from a DNA template. Examples areDNA polymerase I from E. coli, bacteriophage T7 DNA polymerase, or DNApolymerases from bacteriophages T4, Phi-29, M2, or T5. DNA-dependent DNApolymerases may be the naturally occurring enzymes isolated frombacteria or bacteriophages or expressed recombinantly, or may bemodified or “evolved” forms which have been engineered to possesscertain desirable characteristics, e.g., thermostability, or the abilityto recognize or synthesize a DNA strand from various modified templates.All known DNA-dependent DNA polymerases require a complementary primerto initiate synthesis. It is known that under suitable conditions aDNA-dependent DNA polymerase may synthesize a complementary DNA copyfrom an RNA template. RNA-dependent DNA polymerases typically also haveDNA-dependent DNA polymerase activity.

As used herein, a “DNA-dependent RNA polymerase” or “transcriptase” isan enzyme that synthesizes multiple RNA copies from a double-stranded orpartially double-stranded DNA molecule having a promoter sequence thatis usually double-stranded. The RNA molecules (“transcripts”) aresynthesized in the 5′-to-3′ direction beginning at a specific positionjust downstream of the promoter. Examples of transcriptases are theDNA-dependent RNA polymerase from E. coli and bacteriophages T7, T3, andSP6.

As used herein, an “RNA-dependent DNA polymerase” or “reversetranscriptase” (“RT”) is an enzyme that synthesizes a complementary DNAcopy from an RNA template. All known reverse transcriptases also havethe ability to make a complementary DNA copy from a DNA template; thus,they are both RNA- and DNA-dependent DNA polymerases. RTs may also havean RNAse H activity. A primer is required to initiate synthesis withboth RNA and DNA templates.

As used herein, a “selective RNAse” is an enzyme that degrades the RNAportion of an RNA:DNA duplex but not single-stranded RNA,double-stranded RNA or DNA. An exemplary selective RNAse is RNAse H.Enzymes possessing the same or similar activity as RNAse H may also beused. Selective RNAses may be endonucleases or exonucleases. Mostreverse transcriptase enzymes contain an RNAse H activity in addition totheir polymerase activities. However, other sources of the RNAse H areavailable without an associated polymerase activity. The degradation mayresult in separation of RNA from a RNA:DNA complex. Alternatively, aselective RNAse may simply cut the RNA at various locations such thatportions of the RNA melt off or permit enzymes to unwind portions of theRNA. Other enzymes that selectively degrade RNA target sequences or RNAproducts of the present invention will be readily apparent to those ofordinary skill in the art.

The term “specificity,” in the context of an amplification and/ordetection system, is used herein to refer to the characteristic of thesystem which describes its ability to distinguish between target andnon-target sequences dependent on sequence and assay conditions. Interms of nucleic acid amplification, specificity generally refers to theratio of the number of specific amplicons produced to the number ofside-products (e.g., the signal-to-noise ratio). In terms of detection,specificity generally refers to the ratio of signal produced from targetnucleic acids to signal produced from non-target nucleic acids.

The term “sensitivity” is used herein to refer to the precision withwhich a nucleic acid amplification reaction can be detected orquantitated. The sensitivity of an amplification reaction is generally ameasure of the smallest copy number of the target nucleic acid that canbe reliably detected in the amplification system, and will depend, forexample, on the detection assay being employed, and the specificity ofthe amplification reaction, e.g., the ratio of specific amplicons toside-products.

As used herein, a “colony-forming unit” (“CFU”) is used as a measure ofviable microorganisms in a sample. A CFU is an individual viable cellcapable of forming on a solid medium a visible colony whose individualcells are derived by cell division from one parental cell. One CFUcorresponds to ˜1000 copies of rRNA.

As used herein, the term “relative light unit” (“RLU”) is an arbitraryunit of measurement indicating the relative number of photons emitted bythe sample at a given wavelength or band of wavelengths. RLU varies withthe characteristics of the detection means used for the measurement.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a reference sequence for Megasphaera elsdenii 16Sribosomal rRNA gene (SEQ ID NO:45), partial sequence found at GenBankunder accession number AY038996.1 and GI:15145820 (Oct. 15, 2002).

DETAILED DESCRIPTION

The present invention provides compositions, kits and methods foramplifying and detecting Megasphaera sp. nucleic acid from a sample,specifically sequences of Megasphaera 16S rRNA or genes encoding 16SrRNA. Preferably, the samples are biological samples. The compositions,kits and methods provide oligonucleotide sequences that recognize targetsequences of Megasphaera 16S rRNA or their complementary sequences, orgenes encoding 16S rRNA or their complementary sequences. Sucholigonucleotides may be used as amplification oligonucleotides, whichmay include primers, promoter primers, blocked oligonucleotides, andpromoter provider oligonucleotides, whose functions have been describedpreviously (see, e.g., U.S. Pat. Nos. 4,683,195; 4,683,202; 4,800,159;5,399,491; 5,554,516; 5,824,518; and 7,374,885; each incorporated byreference herein). Other oligonucleotides may be used as probes fordetecting amplified sequences of Megasphaera.

The methods provide for the sensitive and specific detection ofMegasphaera nucleic acids. The methods include performing a nucleic acidamplification of Megasphaera sequences and detecting the amplifiedproduct by, for example, specifically hybridizing the amplified productwith a nucleic acid detection probe that provides a signal to indicatethe presence of Megasphaera in the sample. The amplification stepincludes contacting the sample with one or more amplification oligomersspecific for a target sequence in 16S rRNA to produce an amplifiedproduct if Megasphaera nucleic acid is present in the sample.Amplification synthesizes additional copies of the target sequence orits complement by using at least one nucleic acid polymerase to extendthe sequence from an amplification oligomer (a primer) using a templatestrand. One embodiment for detecting the amplified product uses ahybridizing step that includes contacting the amplified product with atleast one probe specific for a sequence amplified by the selectedamplification oligomers, e.g., a sequence contained in the targetsequence flanked by a pair of selected primers.

The detection step may be performed using any of a variety of knowntechniques to detect a signal specifically associated with the amplifiedtarget sequence, such as, e.g., by hybridizing the amplification productwith a labeled detection probe and detecting a signal resulting from thelabeled probe. The detection step may also provide additionalinformation on the amplified sequence, such as, e.g., all or a portionof its nucleic acid base sequence. Detection may be performed after theamplification reaction is completed, or may be performed simultaneouslywith amplifying the target region, e.g., in real time. In oneembodiment, the detection step allows homogeneous detection, e.g.,detection of the hybridized probe without removal of unhybridized probefrom the mixture (see, e.g., U.S. Pat. Nos. 5,639,604 and 5,283,174,each incorporated by reference herein).

In embodiments that detect the amplified product near or at the end ofthe amplification step, a linear detection probe may be used to providea signal to indicate hybridization of the probe to the amplifiedproduct. One example of such detection uses a luminescentally labeledprobe that hybridizes to target nucleic acid. Luminescent label is thenhydrolyzed from non-hybridized probe. Detection is performed bychemiluminescence using a luminometer. (see, e.g., International PatentApplication Pub. No. WO 89/002476, incorporated by reference herein). Inother embodiments that use real-time detection, the detection probe maybe a hairpin probe such as, for example, a molecular beacon, moleculartorch, or hybridization switch probe that is labeled with a reportermoiety that is detected when the probe binds to amplified product. Suchprobes may comprise target-hybridizing sequences andnon-target-hybridizing sequences. Various forms of such probes have beendescribed previously (see, e.g., U.S. Pat. Nos. 5,118,801; 5,312,728;5,925,517; 6,150,097; 6,849,412; 6,835,542; 6,534,274; and 6,361,945;and U.S. Patent Application Pub. Nos. 20060068417A1 and 20060194240A1;each incorporated by reference herein).

A reference sequence for Megasphaera elsdenii 16S ribosomal rRNA gene(SEQ ID NO:45) is shown in FIG. 1. This sequence, from a bovine strainof M. elsdenii, YJ-4, shows a high degree of sequence identity to 16SrRNA sequences from other bovine M. elsdenii strains (see, e.g., Kim etal., J. App. Microbiol. 92:976-982, 2002), and available GenBanksequences from bovine strains of M. elsdenii have been shown to beclosely related to Megasphaera-like species associated with bacterialvaginosis in human (see, e.g., Fredricks et al., N. Eng. J. Med.353:1899-1911, 2005). Thus, the 16S rRNA sequence of SEQ ID NO:45 is aparticularly suitable reference sequence when describing certain aspectsof the present invention herein.

Preferred compositions of the instant invention are configured tospecifically hybridize to a 16S rRNA nucleic acid of Megasphaera sp.with minimal cross-reactivity to other nucleic acids suspected of beingin a sample. In some aspects, the compositions of the instant inventionare configured to specifically hybridize to a 16S rRNA nucleic acid ofMegasphaera sp. with minimal cross-reactivity to one or more ofanaerobic gram-positive cocci; A. vaginae; Lactobacillus sp.;Lactobacillus iners; Lactobacillus crispatus group; Lactobacillusgasseri group; Gardnerella sp.; Gardnerella vaginalis; Trichomonas sp.;Trichomonas vaginalis; Candida sp.; Eggerthella sp.; Bacterium from theorder Clostridiales; Clostridium-like sp.; Prevotella sp.; Prevotellabivia group; Prevotella buccalis group; Atopobium sp.; Atopobiumvaginae; Enterobacteria; Peptostreptococcus micros; Aerococcuschristensenii; Leptotrichia amnionii; Peptoniphilus sp.; Dialister sp.;Mycoplasma hominis; Sneathia sanguinegens; Anaerococcus tetradius;Mobiluncus sp.; Mobiluncus hominis; Eggerthella hongkongensis;Leptotrichia sanguinegens and Finegoldia magna. In one aspect, thecompositions of the instant invention are part of a multiplex systemthat further includes components and methods for detecting one of moreof these organisms.

In certain aspects of the invention, a combination of at least twooligomers is provided for the detection of a Megasphaera sp. 16S rRNA ora gene encoding a Megasphaera sp.16S rRNA. For example, in someembodiments the oligomer combination is for amplification of aMegasphaera target region substantially corresponding to SEQ ID NO:45from about nucleotide position 290 to about nucleotide position 334.Particularly suitable oligomers for the oligomer combination include (1)a first amplification oligomer comprising a target-hybridizing sequencethat is from about 15 to about 25 contiguous nucleotides in length andsubstantially corresponding to, or identical to, a sequence that iscontained in the sequence of SEQ ID NO:34(5′-AGTTGGAGGGGTAACGGCCCAACAAGGCGATGATCAG-3′) and includes at least thesequence of SEQ ID NO:28 (5′-GCCCAACAAGGCGA-3′); and (2) a secondamplification oligomer comprising a target-hybridizing sequence that isfrom about 15 to about 25 contiguous nucleotides in length andsubstantially corresponding to, or identical to, a sequence that iscontained in the sequence of SEQ ID NO:36(5′-CCTCCCGTAGGAGTNTGGGCCGTGTCTCAGTCCC-3′) and includes at least thesequence of SEQ ID NO:35 (5′-GAGTNTGGGCCGTG-3′). In some suchembodiments, the target-hybridizing sequence of the first amplificationoligomer substantially corresponds to, or is identical to, a sequencethat is contained in the sequence of SEQ ID NO:29(5′-GTNACGGCCCARCAAGGCG-AKGATCAG-3′); and/or the target-hybridizingsequence of the second amplification oligomer substantially correspondsto, or is identical to, a sequence that is contained in the sequence ofSEQ ID NO:33 (5′-CGTAGGAGTNTGGGCCGTGTCTCAG-3′). In other embodiments ofan oligomer combination as above, the target-hybridizing sequence of thesecond amplification oligomer substantially corresponds to, or isidentical to, a sequence that includes at least the sequence of SEQ IDNO:32 (5′-GTAGGAGTNTGGGCCGTGTCTC-3′). In specific variations, thetarget-hybridizing sequence of the first amplification oligomer consistsof a sequence substantially corresponding to, or identical to, thesequence shown in SEQ ID NO:13 (5′-GTAACGGCCCAACAAGGCGA-3′) or SEQ IDNO:14 (5′-GCCCAACAAGGCGATGATCAG-3′); and/or the target-hybridizingsequence of the second amplification oligomer consists of a sequencesubstantially corresponding to, or identical to, the sequence shown inSEQ ID NO:19 (5′-GTAGGAGTCTGGGCCGTGTCTCAG-3′) or SEQ ID NO:20(5′-CGTAGGAGTCTGGGCCGTGTCTC-3′).

In other embodiments, the oligomer combination is for amplification of aMegasphaera target region substantially corresponding to SEQ ID NO:45from about nucleotide position 466 to about nucleotide position 607.Particularly suitable oligomers for the oligomer combination include (1)a first amplification oligomer comprising a target-hybridizing sequencethat is from about 15 to about 25 contiguous nucleotides in length andsubstantially corresponding to, or identical to, a sequence that iscontained in the sequence of SEQ ID NO:38(5′-GGTTGTAAAGTTCTGTTATACGGGACGAATGG-3′) and includes at least thesequence of SEQ ID NO:37 (5′-CTGTTATACGGGAC-3′); and (2) a secondamplification oligomer comprising a target-hybridizing sequence that isfrom about 15 to about 25 contiguous nucleotides in length andsubstantially corresponding to, or identical to, a sequence that iscontained in the sequence of SEQ ID NO:40(5′-GCCCCGCACTTTTAAGACCGACTTACGACGC-3′) and includes at least thesequence of SEQ ID NO:39 (5′-CTTTTAAGACCGAC-3′). In specific variations,the target-hybridizing sequence of the first amplification oligomerconsists of a sequence substantially corresponding to, or identical to,the sequence shown in SEQ ID NO:15 (5′-CTGTTATACGGGACGAAT-3′); and/orthe target-hybridizing sequence of the second amplification oligomerconsists of a sequence substantially corresponding to, or identical to,the sequence shown in SEQ ID NO:21 (5′-CCGCACTTTTAAGACCGACTTA-3′).

In certain embodiments, an amplification oligomer as described herein isa promoter primer further comprising a promoter sequence located 5′ tothe target-hybridizing sequence and which is non-complementary to theMegasphaera target nucleic acid. For example, in some embodiments of anoligomer combination as described herein for amplification of aMegasphaera target region substantially corresponding to SEQ ID NO:45from about nucleotide position 290 to about nucleotide position 334 orfrom about nucleotide position 466 to about nucleotide position 607, thesecond amplification oligomer is a promoter primer further comprising a5′ promoter sequence. In particular embodiments, the promoter sequenceis a T7 RNA polymerase promoter sequence such as, for example, a T7promoter sequence having the sequence shown in SEQ ID NO:22(5′-AATTTAATACGACTCACTATAGGGAGA-3′). In specification variations of anoligomer combination as described herein for amplification of aMegasphaera target region substantially corresponding to SEQ ID NO:45from about nucleotide position 290 to about nucleotide position 334, thesecond amplification oligomer is a promoter primer having the sequenceshown in SEQ ID NO:16(5′-AATTTAATACGACTCACTATAGGGAGAGTAGGAGTCTGGGCCGTGTCTCAG-3′) or SEQ IDNO:17 (5′-AATTTAATACGACTCACTATAGGGAGACGTAGGAGTCTGGGCCGTGTCTC-3′). Inspecific variations of an oligomer combination as described herein foramplification of a Megasphaera target region substantially correspondingto SEQ ID NO:45 from about nucleotide position 466 to about nucleotideposition 607, the second amplification oligomer is a promoter primerhaving the sequence shown in SEQ ID NO:18(5′-AATTTAATACGACTCACTATAGGGAGACCGCACTTTTAAGACCGACTTA-3′).

In some embodiments, an oligomer combination as described herein furthercomprises at least one capture probe oligomer comprising atarget-hybridizing sequence substantially corresponding to a sequencecontained in the complement of SEQ ID NO:45, wherein thetarget-hybridizing sequence is covalently attached to a sequence ormoiety that binds to an immobilized probe. In specific variations, thetarget-hybridizing sequence comprises or consists of a sequencesubstantially corresponding to, or identical to, a sequence selectedfrom SEQ ID NO:7 (5′-CTACTGCTGCCTCCCGTAGGAG-3′), SEQ ID NO:8(5′-GGACTACCAGGG TATCTAATCCTG-3′), SEQ ID NO:9(5′-CGACACGAGCTGACGACAGCCATGCA-3′), SEQ ID NO:10(5′-GACGTCATCCCCACCTTCCT-3′), SEQ ID NO:11(5′-CGTATTCGGTATTAGCAGCCG-3′), and SEQ ID NO:12(5′-GCTGGCACGTAGTTAGCCGTGGCT-3′). Particularly suitable capture probesfor use in accordance with the present invention comprise or consist ofa sequence selected from SEQ ID NO:1(5′-CTACTGCTGCCTCCCGTAGGAGTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′), SEQ IDNO:2 (5′-GGACTACCAGGGTATCTAATCCTGTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′),SEQ ID NO:3 (5′-CGACACGAGCTGACGACAGCCATGCATTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′), SEQ ID NO:4 (5′-GACGTCATCCCCACCTTCCTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′), SEQ ID NO:5 (5′-CGTATTCGGTATTAGCAGCCGTTTAAAAAAAAAAAAAAAAAAAAAAAAAAA AAA-3′), and SEQ ID NO:6(5′-GCTGGCACGTAGTTAGCCGTGGCTTTTAAAA AAAAAAAAAAAAAA AAAAAAAAAAAA-3′).

In certain variations, an oligomer combination as described hereinfurther comprises at least one detection probe oligomer configured tospecifically hybridize to a Megasphaera target sequence that isamplifiable using the first and second amplification oligomers (e.g., aMegasphaera target sequence that is flanked by the target-hybridizingsequences of the first and second amplification oligomers). In someembodiments, a detection probe oligomer for use in accordance with thepresent invention comprises a target-hybridizing sequence that is fromabout 14 to about 40 nucleotides in length and is configured tospecifically hybridize to a target sequence contained within aMegasphaera target region from about nucleotide position 290 to aboutnucleotide position 334 of SEQ ID NO:45. For example, in somevariations, the detection probe oligomer comprises a target- hybridizingsequence substantially corresponding to, or identical to, a sequencethat is contained in the sequence of SEQ ID NO:31(5′-CAGTAGCCGGTCTGAGAGGATGAACG-3′) and includes at least the sequence ofSEQ ID NO:30 (5′-GTAGCCGGTCTGAGAGGATGA-3′). Particularly suitabledetection probe oligomers include, for example, oligomers comprising atarget-hybridizing sequence substantially corresponding to, or identicalto, a sequence selected from SEQ ID NO:23(5′-CAGTAGCCGGTCTGAGAGGATGA-3′) and SEQ ID NO:25 (5′-GTAGCCGGTCTGAGAGGATGAACG-3′).

In other embodiments, a detection probe oligomer for use in accordancewith the present invention comprises a target-hybridizing sequence thatis from about 14 to about 40 nucleotides in length and is configured tospecifically hybridize to a target sequence contained within aMegasphaera target region from about nucleotide position 466 to aboutnucleotide position 607 of SEQ ID NO:45, or to a target sequencecontained within a Megasphaera target region from about nucleotideposition 466 to about nucleotide position 536 of SEQ ID NO:45. Forexample, in some variations, the detection probe oligomer comprises atarget-hybridizing sequence substantially corresponding to, or identicalto, a sequence that is contained in the sequence of SEQ ID NO:24(5′-GACGGTACCGTAAGAGAAAGCC-3′) and includes at least the sequence of SEQID NO:26 (5′-CGGTACCGTAAGAGAAAG-3′). Particularly suitable detectionprobe oligomers include, for example, oligomers comprising atarget-hybridizing sequence substantially corresponding to, or identicalto, a sequence selected from SEQ ID NO:24 and SEQ ID NO:26.

Typically, a detection probe oligomer in accordance with the presentinvention further includes a label. Particularly suitable labels includecompounds that emit a detectable light signal, e.g., fluorophores orluminescent (e.g., chemiluminescent) compounds that can be detected in ahomogeneous mixture. More than one label, and more than one type oflabel, may be present on a particular probe, or detection may rely onusing a mixture of probes in which each probe is labeled with a compoundthat produces a detectable signal (see, e.g., U.S. Pat. Nos. 6,180,340and 6,350,579, each incorporated by reference herein). Labels may beattached to a probe by various means including covalent linkages,chelation, and ionic interactions, but preferably the label iscovalently attached. For example, in some embodiments, a detection probehas an attached chemiluminescent label such as, e.g., an acridiniumester (AE) compound (see, e.g., U.S. Pat. Nos. 5,185,439; 5,639,604;5,585,481; and 5,656,744; each incorporated by reference herein), whichin typical variations is attached to the probe by a non-nucleotidelinker (see, e.g., U.S. Pat. Nos. 5,585,481; 5,656,744; and 5,639,604,particularly at column 10, line 6 to column 11, line 3, and Example 8;each incorporated by reference herein). In other embodiments, adetection probe comprises both a fluorescent label and a quencher, acombination that is particularly useful in fluorescence resonance energytransfer (FRET) assays. Specific variations of such detection probesinclude, e.g., a TaqMan detection probe (Roche Molecular Diagnostics)and a “molecular beacon” (see, e.g., Tyagi et al., Nature Biotechnol.16:49-53, 1998; U.S. Pat. Nos. 5,118,801 and 5,312,728; eachincorporated by reference herein).

A detection probe oligomer in accordance with the present invention mayfurther include a non-target-hybridizing sequence. Specific embodimentsof such detection probes include, for example, probes that formconformations held by intramolecular hybridization, such asconformations generally referred to as hairpins. Particularly suitablehairpin probes include a “molecular torch” (see, e.g., U.S. Pat. Nos.6,849,412; 6,835,542; 6,534,274; and 6,361,945, each incorporated byreference herein) and a “molecular beacon” (see, e.g., Tyagi et al.,supra; U.S. Pat. No. 5,118,801 and U.S. Pat. No. 5,312,728, supra).Methods for using such hairpin probes are well known in the art.

In yet other embodiments, a detection probe is a linear oligomers thatdoes not substantially form conformations held by intramolecular bonds.In specific variations, a linear detection probe oligomer includes achemiluminescent compound as the label, preferably an AE compound.

In yet other variations, an oligomer combination for detection of aMegasphaera nucleic acid further comprises a pseudotarget oligomer thatcan be amplified using first and second amplification oligomers asdescribed herein. Typically, the pseudotarget oligomer is sufficientlydistinct from the target region of Megasphaera nucleic acid flanked bythe amplification oligomers, such that a detection probe configured tospecifically hybridize to a Megasphaera-specific amplification product,generated using the amplification oligomers on a Megasphaera targetnucleic acid template, will not specifically hybridize to anamplification product generated using the same amplification oligomerswith the pseudotarget oligomer template. Pseudotargets may be used toadjust assay sensitivity by changing the cutoff used to classify asample as positive or negative, rather than re-optimizing the entire ampsystem to get lower sensitivity through lower amplification efficiency.Accordingly, such pseudotarget oligomers are particularly useful for“detuning” assay sensitivity in certain embodiments of the detectionmethods described herein. In a specific embodiment, the pseudotargetoligomer has a sequence substantially corresponding to, or identical to,a sequence selected from SEQ ID NO:27(5′-CTGTTATACGGGACGAATTAAGTCGGTCTTAAAAGTGCGG-3′) (amplifiable using,e.g., amplification oligomers comprising target-hybridizing sequences ofSEQ ID NOs:15 and 18); SEQ ID NO:41(5′-GTAACGGCCCAACAAGGCGACTGAGACACGGCCCAGACTCCTAC-3′) (amplifiable using,e.g., amplification oligomers comprising target-hybridizing sequences ofSEQ ID NOs:13 and 19); SEQ ID NO:42(5′-GTAACGGCCCAACAAGGCGAGAGACACGGCCCAGACTCCTACG-3′) (amplifiable using,e.g., amplification oligomers comprising target-hybridizing sequences ofSEQ ID NOs:13 and 20); SEQ ID NO:43(5′-GCCCAACAAGGCGATGATCAGCTGAGACACGGCCCAGACTCCTAC-3′) (amplifiableusing, e.g., amplification oligomers comprising target-hybridizingsequences of SEQ ID NOs:14 and 19); and SEQ ID NO:44(5′-GCCCAACAAGGCGATGATCAGGAGACACGGCCCAGACTCCTACG-3′) (amplifiable using,e.g., amplification oligomers comprising target-hybridizing sequences ofSEQ ID NOs:14 and 20).

Also provided by the present invention are detection probe oligomers,capture probe oligomers, and pseudotarget oligomers as described herein.

In another aspect, the present invention provides methods for detectinga Megasphaera sp. 16S rRNA or a gene encoding a Megasphaera sp. 16S rRNAin a sample using a combination of at least two oligomers as describedherein. Such a method generally includes (a) providing a samplesuspected of containing a Megasphaera sp. bacterium; (b) contacting thesample with at least two oligomers for amplifying a Megasphaera sp.nucleic acid target region corresponding to a Megasphaera 16S rRNAtarget nucleic acid, where the oligomer combination includes first andsecond amplification oligomers as described above for either a first orsecond target region; (c) performing an in vitro nucleic acidamplification reaction, where any Megasphaera target nucleic acidpresent in the sample is used as a template for generating anamplification product; and (d) detecting the presence or absence of theamplification product, thereby indicating the presence or absence ofMegasphaera sp. in the sample.

In certain embodiments, the method further includes purifying theMegasphaera target nucleic acid from other components in the samplebefore the amplification step. Such purification may include may includemethods of separating and/or concentrating organisms contained in asample from other sample components. In particular embodiments,purifying the target nucleic acid includes capturing the target nucleicacid to specifically or non-specifically separate the target nucleicacid from other sample components. Non- specific target capture methodsmay involve selective precipitation of nucleic acids from asubstantially aqueous mixture, adherence of nucleic acids to a supportthat is washed to remove other sample components, or other means ofphysically separating nucleic acids from a mixture that containsMegasphaera nucleic acid and other sample components.

In some embodiments, a 16S rRNA target nucleic of Megasphaera sp. or agene encoding the 16S rRNA of Megasphaera is selectively separated fromother sample components by specifically hybridizing the Megasphaeratarget nucleic acid to a capture probe oligomer. The capture probeoligomer comprises a target- hybridizing sequence configured tospecifically hybridize to a Megasphaera 16S rRNA target sequence so asto form a target-sequence:capture-probe complex that is separated fromsample components. Suitable capture probe target-hybridizing sequencesinclude, e.g., the sequences shown in SEQ ID NOs:7-12. In a preferredvariation, the specific target capture binds the Megasphaera 16S rRNAtarget:capture-probe complex to an immobilized probe to form atarget:capture-probe:immobilized-probe complex that is separated fromthe sample and, optionally, washed to remove non-target samplecomponents (see, e.g., U.S. Pat. Nos. 6,110,678; 6,280,952; and6,534,273; each incorporated by reference herein). In such variations,the capture probe oligomer further comprises a sequence or moiety thatbinds attaches the capture probe, with its bound target sequence, to animmobilized probe attached to a solid support, thereby permitting thehybridized target nucleic acid to be separated from other samplecomponents.

In more specific embodiments, the capture probe oligomer includes a tailportion (e.g., a 3′ tail) that is not complementary to the Megasphaerasp. 16S rRNA target sequence but that specifically hybridizes to asequence on the immobilized probe, thereby serving as the moietyallowing the target nucleic acid to be separated from other samplecomponents, such as previously described in, e.g., U.S. Pat. No.6,110,678, incorporated herein by reference. Any sequence may be used ina tail region, which is generally about 5 to 50 nt long, and preferredembodiments include a substantially homopolymeric tail of about 10 to 40nt (e.g., A₁₀ to A₄₀), more preferably about 14 to 33 nt (e.g., A₁₄ toA₃₀ or T₃A₁₄ to T₃A₃₀), that bind to a complementary immobilizedsequence (e.g., poly-T) attached to a solid support, e.g., a matrix orparticle. For example, in specific embodiments of a capture probecomprising a 3′ tail, the capture probe has a sequence selected from SEQID NOs:1-6.

Target capture typically occurs in a solution phase mixture thatcontains one or more capture probe oligomers that hybridize specificallyto the 16S rRNA of Megasphaera sp. or gene target sequence underhybridizing conditions, usually at a temperature higher than the T_(m)of the tail-sequence:immobilized-probe-sequence duplex. For embodimentscomprising a capture probe tail, the Megasphaera-165-rRNA-target:capture-probe complex is captured by adjusting the hybridizationconditions so that the capture probe tail hybridizes to the immobilizedprobe, and the entire complex on the solid support is then separatedfrom other sample components. The support with the attachedimmobilized-probe:capture-probe:Megasphaera-16S-rRNA-target-sequence maybe washed one or more times to further remove other sample components.Preferred embodiments use a particulate solid support, such asparamagnetic beads, so that particles with the attachedMegasphaera-16S-rRNA-target:capture-probe:immobilized-probe complex maybe suspended in a washing solution and retrieved from the washingsolution, preferably by using magnetic attraction. To limit the numberof handling steps, the Megasphaera sp. 16S rRNA target nucleic acid maybe amplified by simply mixing the Megasphaera 16S rRNA target sequencein the complex on the support with amplification oligomers andproceeding with amplification steps.

Amplifying a Megasphaera target sequence utilizes an in vitroamplification reaction using at least two amplification oligomers thatflank a target region to be amplified. In particular embodiments, thetarget region to be amplified substantially corresponds to SEQ ID NO:45from about nucleotide position 290 about nucleotide position 334, orfrom about nucleotide position 466 to about 607. Particularly suitableamplification oligomer combinations for amplification of these targetregions are described herein (see, e.g., paragraphs [85]-[87], supra).Suitable amplification methods include, for example, replicase-mediatedamplification, polymerase chain reaction (PCR), ligase chain reaction(LCR), strand-displacement amplification (SDA), and transcription-mediated or transcription-associated amplification (TMA). Suchamplification methods are well-known in the art (see, e.g., paragraphs[56] and [57], supra) and are readily used in accordance with themethods of the present invention.

For example, amplification methods that use TMA amplification includethe following steps. Briefly, the target nucleic acid that contains thesequence to be amplified is provided as single stranded nucleic acid(e.g., ssRNA or ssDNA). Those skilled in the art will appreciate thatconventional melting of double stranded nucleic acid (e.g., dsDNA) maybe used to provide single-stranded target nucleic acids. A promoterprimer binds specifically to the target nucleic acid at its targetsequence and a reverse transcriptase (RT) extends the 3′ end of thepromoter primer using the target strand as a template to create a cDNAcopy of the target sequence strand, resulting in an RNA:DNA duplex. AnRNase digests the RNA strand of the RNA:DNA duplex and a second primerbinds specifically to its target sequence, which is located on the cDNAstrand downstream from the promoter primer end. RT synthesizes a new DNAstrand by extending the 3′ end of the second primer using the first cDNAtemplate to create a dsDNA that contains a functional promoter sequence.An RNA polymerase specific for the promoter sequence then initiatestranscription to produce RNA transcripts that are about 100 to 1000amplified copies (“amplicons”) of the initial target strand in thereaction. Amplification continues when the second primer bindsspecifically to its target sequence in each of the amplicons and RTcreates a DNA copy from the amplicon RNA template to produce an RNA:DNAduplex. RNase in the reaction mixture digests the amplicon RNA from theRNA:DNA duplex and the promoter primer binds specifically to itscomplementary sequence in the newly synthesized DNA. RT extends the 3′end of the promoter primer to create a dsDNA that contains a functionalpromoter to which the RNA polymerase binds to transcribe additionalamplicons that are complementary to the target strand. The autocatalyticcycles of making more amplicon copies repeat during the course of thereaction resulting in about a billion-fold amplification of the targetnucleic acid present in the sample. The amplified products may bedetected in real-time during amplification, or at the end of theamplification reaction by using a probe that binds specifically to atarget sequence contained in the amplified products. Detection of asignal resulting from the bound probes indicates the presence of thetarget nucleic acid in the sample.

Detection of the amplified products may be accomplished by a variety ofmethods. The nucleic acids may be associated with a surface that resultsin a physical change, such as a detectable electrical change. Amplifiednucleic acids may be detected by concentrating them in or on a matrixand detecting the nucleic acids or dyes associated with them (e.g., anintercalating agent such as ethidium bromide or cyber green), ordetecting an increase in dye associated with nucleic acid in solutionphase. Other methods of detection may use nucleic acid detection probesthat are configured to specifically hybridize to a sequence in theamplified product and detecting the presence of the probe:productcomplex, or by using a complex of probes that may amplify the detectablesignal associated with the amplified products (e.g., U.S. Pat. Nos.5,424,413; 5,451,503; and 5,849,481; each incorporated by referenceherein). Directly or indirectly labeled probes that specificallyassociate with the amplified product provide a detectable signal thatindicates the presence of the target nucleic acid in the sample. Forexample, if the target nucleic acid is the 16S rRNA of Megasphaera sp.,the amplified product will contain a target sequence in or complementaryto a sequence in the 16S rRNA of Megasphaera, and a probe will binddirectly or indirectly to a sequence contained in the amplified productto indicate the presence of the 16S rRNA of Megasphaera in the testedsample.

Preferred embodiments of detection probes that hybridize to thecomplementary amplified sequences may be DNA or RNA oligomers, oroligomers that contain a combination of DNA and RNA nucleotides, oroligomers synthesized with a modified backbone, e.g., an oligomer thatincludes one or more 2′ - methoxy substituted ribonucleotides. Probesused for detection of the amplified Megasphaera sp. rRNA sequences maybe unlabeled and detected indirectly (e.g., by binding of anotherbinding partner to a moiety on the probe) or may be labeled with avariety of detectable labels. Particular embodiments of detection probessuitable for use in accordance with methods of the present invention arefurther described herein (see, e.g., paragraphs [91]-[93], supra).

Oligomers that are not intended to be extended by a nucleic acidpolymerase preferably include a blocker group that replaces the 3′ OH toprevent enzyme-mediated extension of the oligomer in an amplificationreaction. For example, blocked amplification oligomers and/or detectionprobes present during amplification preferably do not have a functional3′ OH and instead include one or more blocking groups located at or nearthe 3′ end. A blocking group near the 3′ end is preferably within fiveresidues of the 3′ end and is sufficiently large to limit binding of apolymerase to the oligomer, and other preferred embodiments contain ablocking group covalently attached to the 3′ terminus. Many differentchemical groups may be used to block the 3′ end, e.g., alkyl groups,non-nucleotide linkers, alkane-diol dideoxynucleotide residues, andcordycepin. A preferred method for detecting Megasphaera sp. 16S rRNAsequences uses a transcription-associated amplification with a linearchemiluminescently labeled probe, more preferably, a linear AE labeledprobe.

Assays for detection of the Megasphaera sp. 16S rRNA nucleic acid mayoptionally include a non-Megasphaera sp. 16S rRNA internal control (IC)nucleic acid that is amplified and detected in the same assay reactionmixtures by using amplification and detection oligomers specific for theIC sequence. IC nucleic acid sequences can be synthetic nucleic acidsequences that are spiked into a sample or the IC nucleic acid sequencesmay be cellular component. IC nucleic acid sequences that are cellularcomponents can be from exogenous cellular sources or endogenous cellularsources relative to the specimen. An exogenous cellular source, forexample, is a cell that is added into the sample and that then flowsthrough the sample processing procedures along with the specimen. A moreparticular example would be the addition of a HeLa cell, Jurkat cell,SiLa cell or other to the sample medium along with the specimen that iscollected for testing (e.g., a vaginal swab specimen). The specimen andthe exogenous cells are then processed, amplified and detected. Thespecimen being amplified and detected using amplification and detectionoligomers for identifying the target sequence of interest and theexogenous cells being amplified and detected using amplification anddetection oligomers for identifying an IC target sequence such as 18SrRNA. An endogenous cellular source is a cellular source that wouldnaturally be obtained when gathering the specimen. One example:epithelial cells will present when obtaining a specimen via a vaginalswab. Similar then to the above exemplary exogenous cells processdescribed, the specimen and the endogenous cellular source are bothprocessed, amplified, and detected. The specimen being amplified anddetected using amplification and detection oligomers for identifying thetarget sequence of interest and the endogenous cells being amplified anddetected using amplification and detection oligomers for identifying anIC target sequence; typically a housekeeping gene present in theendogenous cellular source, such as a beta-globulin gene. (See e.g.,Poljak et al., J. Clin. Virol, 25: S89-97, 2002; U.S. Pat. No.6,410,321; and U.S. Patent Application Publication No. 2004-0023288;each incorporated by reference herein). Use of a cellular source ICallows for a control from sample collection through detection. Syntheticnucleic acid sequences provide for control of amplification anddetection.

In certain embodiments, amplification and detection of a signal from theamplified IC sequence demonstrates that the assay reagents, conditions,and performance of assay steps were properly used in the assay if nosignal is obtained for the intended target Megasphaera sp. nucleic acid(e.g., samples that test negative for the 16S rRNA of Megasphaera sp.).An IC may also be used as an internal calibrator for the assay when aquantitative result is desired, i.e., the signal obtained from the ICamplification and detection is used to set a parameter used in analgorithm for quantitating the amount of Megasphaera nucleic acid in asample based on the signal obtained for amplified an Megasphaera 16SrRNA target sequence. ICs are also useful for monitoring the integrityof one or more steps in an assay. A preferred embodiment of a syntheticIC nucleic acid sequence is a randomized sequence that has been derivedfrom a naturally occurring source (e.g., an HIV sequence that has beenrearranged in a random manner). Another preferred IC nucleic acidsequence may be an RNA transcript isolated from a naturally occurringsource or synthesized in vitro, such as by making transcripts from acloned randomized sequence such that the number of copies of IC includedin an assay may be accurately determined. The primers and probe for theIC target sequence are configured and synthesized by using anywell-known method provided that the primers and probe function foramplification of the IC target sequence and detection of the amplifiedIC sequence using substantially the same assay conditions used toamplify and detect the Megasphaera target sequence. In preferredembodiments that include a target capture-based purification step, it ispreferred that a target capture probe specific for the IC target beincluded in the assay in the target capture step so that the IC istreated in the assay in a manner analogous to that for the intendedMegasphaera analyte in all of the assay steps.

Assays for detection of the Megasphaera sp. 16S rRNA nucleic acid mayoptionally include a pseudotarget. A “pseudotarget” is anoligonucleotide that can be co-amplified with the target polynucleotidein a single amplification reaction. The pseudotarget and targetpolynucleotide may be amplified using the same set of oligonucleotideprimers. The pseudotarget and the target polynucleotide will benon-identical molecules so that the target probe will not detect thepseudotarget.

Amplification methods using pseudotargets are useful for quantifyingtarget polynucleotides present in a test sample. These methods includessteps for: (1) obtaining a test sample that contains an unknown amountof an target polynucleotide; (2) combining a predetermined amount ofthis test sample with a predetermined amount of a pseudotarget; (3)co-amplifying in an amplification reaction the target polynucleotide andthe pseudotarget to produce a collection of amplification products thatincludes both a target amplicon and a pseudotarget amplicon; and (4)quantifying the target amplicon without relying on information regardingthe amount of pseudotarget amplicon produced in the reaction, wherebythe quantity of target amplicon is related in a dose-dependent manner tothe unknown amount target polynucleotide that was present in theoriginal test sample. Amplification reactions that include apseudotarget have been shown under certain conditions to provide uniformresults having less variability than similar amplification reactionslacking pseudotarget. This is particularly true for amplification ofsamples containing a low level of target nucleic acid. Using apseudotarget in an amplification reaction changes the probe RLU outputfrom an all-or-none response to a response wherein the RLU output isproportional to target input. Thus, pseudotarget allows for adjustmentsin assay sensitivity by changing the cutoff used to classify a sample aspositive or negative, rather than re-optimizing the entire amp system toget lower sensitivity through lower amplification efficiency.Pseudotargets are further advantageous for detecting low-levels oftarget nucleic acid in a specimen. (See also U.S. Pat. No. 6,294,338,incorporated by reference herein).

Detecting Megasphaera sp. to diagnosis bacterial vaginosis in a clinicalsample will preferably use higher RLU cut-off values than those used fordetecting the presence/absence of A. vaginae from a sample. This isbecause for diagnosis of BV, normal samples can be positive forrelatively low amounts of Megasphaera sp. while BV samples will haverelatively greater amounts of Megasphaera sp. So for diagnosis, a higherRLU cut-off value is one approach to differentiating normal levels ofMegasphaera from elevated levels present in a sample. Depending on thedesired application for the amplification and detection oligomersdescribed herein, a skilled artisan will set an appropriate RLU cut-offvalue, with lower values being useful for detecting all Megasphaera sp.present in a sample, and higher RLU values being useful for detecting athreshold amount of Megasphaera sp. in a sample.

Additional microbe detection assays can be similarly performed fordetermining the presence and/or relative amount of a plurality ofmicrobes implicated in BV. By way of example only, such plurality ofmicrobes can include one or more of anerobic gram-positive cocci;Atopobium vaginae; Lactobacillus sp.; Lactobacillus iners; Lactobacilluscrispatus group; Lactobacillus gasseri group; Gardnerella sp.;Gardnerella vaginalis; Trichomonas sp.; Trichomonas vaginalis; Candidasp.; Eggerthella sp.; Bacterium from the order Clostridiales;Clostridium-like sp.; Prevotella sp.; Prevotella bivia group; Prevotellabuccalis group; Atopobium sp.; Atopobium vaginae; Enterobacteria;Peptostreptococcus micros; Aerococcus christensenii; Leptotrichiaamnionii; Peptoniphilus sp.; Dialister sp.; Mycoplasma hominis; Sneathiasanguinegens; Anaerococcus tetradius; Mobiluncus sp.; Mobiluncushominis; Eggerthella hongkongensis; Leptotrichia sanguinegens andFinegoldia magna. Assays may be performed separately or multiplexed.Thus, a diagnosis of BV can include identifying a plurality of microbesand optionally determining their relative abundances in a sample.

Also provided by the subject invention is a reaction mixture foramplification and/or detection of a Megasphaera sp. target nucleic acid.A reaction mixture in accordance with the present invention at leastcomprises one or more of the following: an oligomer combination asdescribed herein for amplification of a Megasphaera target nucleic acid;a capture probe oligomer as described herein for purifying theMegasphaera target nucleic acid; a detection probe oligomer as describedherein for determining the presence or absence of a Megasphaeraamplification product; and a pseudotarget oligomer as described hereinfor detuning sensitivity of an assay for detecting the Megasphaeratarget nucleic acid. The reaction mixture may further include a numberof optional components such as, for example, arrays of capture probenucleic acids. For an amplification reaction mixture, the reactionmixture will typically include other reagents suitable for performing invitro amplification such as, e.g., buffers, salt solutions, appropriatenucleotide triphosphates (e.g., dATP, dCTP, dGTP, dTTP, ATP, CTP, GTPand UTP), and/or enzymes (e.g., reverse transcriptase, and/or RNApolymerase), and will typically include test sample components, in whicha Megasphaera target nucleic acid may or may not be present. Inaddition, for a reaction mixture that includes a detection probetogether with an amplification oligomer combination, selection ofamplification oligomers and detection probe oligomers for a reactionmixture are linked by a common target region (i.e., the reaction mixturewill include a probe that binds to a sequence amplifiable by anamplification oligomer combination of the reaction mixture).

Also provided by the subject invention are kits for practicing themethods as described herein. A kit in accordance with the presentinvention at least comprises one or more of the following: anamplification oligomer combination as described herein for amplificationof a Megasphaera target nucleic acid; a capture probe oligomer asdescribed herein for purifying the Megasphaera target nucleic acid; adetection probe oligomer as described herein for determining thepresence or absence of a Megasphaera amplification product; and apseudotarget oligomer as described herein for detuning sensitivity of anassay for detecting the Megasphaera target nucleic acid. The kits mayfurther include a number of optional components such as, for example,arrays of capture probe nucleic acids. Other reagents that may bepresent in the kits include reagents suitable for performing in vitroamplification such as, e.g., buffers, salt solutions, appropriatenucleotide triphosphates (e.g., dATP, dCTP, dGTP, dTTP, ATP, CTP, GTPand UTP), and/or enzymes (e.g., reverse transcriptase, and/or RNApolymerase). Oligomers as described herein may be packaged in a varietyof different embodiments, and those skilled in the art will appreciatethat the invention embraces many different kit configurations. Forexample, a kit may include amplification oligomers for only one targetregion of a Megasphaera sp. genome, or it may include amplificationoligomers for multiple Megasphaera sp. target regions. In addition, fora kit that includes a detection probe together with an amplificationoligomer combination, selection of amplification oligomers and detectionprobe oligomers for a kit are linked by a common target region (i.e.,the kit will include a probe that binds to a sequence amplifiable by anamplification oligomer combination of the kit). In certain embodiments,the kit further includes a set of instructions for practicing methods inaccordance with the present invention, where the instructions may beassociated with a package insert and/or the packaging of the kit or thecomponents thereof.

The invention is further illustrated by the following non-limitingexamples.

EXAMPLE 1 Reagents

Various reagents are identified in the examples below. The formulationsand pH values (where relevant) of these reagents were as follows.

A “Lysis Buffer” contains 15 mM sodium phosphate monobasic monohydrate,15 mM sodium phosphate dibasic anhydrous, 1.0 mM EDTA disodiumdihydrate, 1.0 mM EGTA free acid, and 110 mM lithium lauryl sulfate, pH6.7.

A “Urine Lysis Buffer” contains 150 mM HEPES free acid, 294 mM lithiumlauryl sulfate, 57 mM lithium hydroxide monohydrate, 100 mM ammoniumsulfate, pH 7.5.

A “Target Capture Reagent” contains 250 mM HEPES free acid dihydrate,310 mM lithium hydroxide monohydrate, 1.88 M lithium chloride, 100 mMEDTA free acid, 2 M lithium hydroxide to pH 6.4, and 250 ng/ml 1 micronmagnetic particles Sera-Mag™ MG-CM Carboxylate Modified (Seradyn, Inc.;Indianapolis, Ind.; Cat. No. 24152105-050450) having oligo(dT)₁₄covalently bound thereto.

A “Wash Solution” contains 10 mM HEPES free acid, 6.5 mM sodiumhydroxide, 1 mM EDTA free acid, 0.3% (v/v) ethyl alcohol absolute, 0.02%(w/v) methyl paraben, 0.01% (w/v) propyl paraben, 150 mM sodiumchloride, 0.1% (w/v) lauryl sulfate, sodium (SDS), and 4 M sodiumhydroxide to pH 7.5.

An “Amplification Reagent” is a lyophilized form of a 3.6 mL solutioncontaining 26.7 mM rATP, 5.0 mM rCTP, 33.3 mM rGTP and 5.0 mM rUTP, 125mM HEPES free acid, 8% (w/v) trehalose dihydrate, 1.33 mM dATP, 1.33 mMdCTP, 1.33 mM dGTP, 1.33 mM dTTP, and 4 M sodium hydroxide to pH 7.5.The Amplification Reagent is reconstituted in 9.7 mL of “AmplificationReagent Reconstitution Solution” described below.

An “Amplification Reagent Reconstitution Solution” contains 0.4% (v/v)ethyl alcohol absolute, 0.10% (w/v) methyl paraben, 0.02% (w/v) propylparaben, 33 mM KCl, 30.6 mM MgCl₂, 0.003% phenol red.

A “Primer Reagent” contains 1 mM EDTA disodium dihydrate, ACS, 10 mMTrizma7 base, and 6 M hydrochloric acid to pH 7.5.

An “Enzyme Reagent” is a lyophilized form of a 1.45 mL solutioncontaining 20 mM HEPES free acid dihydrate, 125 mM N-acetyl-L-cysteine,0.1 mM EDTA disodium dihydrate, 0.2% (v/v) TRITON® X-100 detergent, 0.2M trehalose dihydrate, 0.90 RTU/mL Moloney murine leukemia virus(“MMLV”) reverse transcriptase, 0.20 U/mL T7 RNA polymerase, and 4 Msodium hydroxide to pH 7.0. (One “unit” or “RTU” of activity is definedas the synthesis and release of 5.75 fmol cDNA in 15 minutes at 37° C.for MMLV reverse transcriptase, and for T7 RNA polymerase, one “unit” or“U” of activity is defined as the production of 5.0 fmol RNA transcriptin 20 minutes at 37° C.) The Enzyme Reagent is reconstituted in 3.6 mLof “Enzyme Reagent Reconstitution Solution” described below.

An “Enzyme Reagent Reconstitution Solution” contains 50 mM HEPES freeacid, 1 mM EDTA free acid, 10% (v/v) TRITON X-100 detergent, 120 mMpotassium chloride, 20% (v/v) glycerol anhydrous, and 4 M sodiumhydroxide to pH 7.0.

A “Probe Reagent” is a lyophilized form of a 3.6mL solution containing110 mM lithium lauryl sulfate, 10 mM of mercaptoethane sulfonic acid,100 mM lithium succinate, and 3% PVP. The Probe Reagent is reconstitutedin 36 mL of “Probe Reagent Reconstitution Solution” described below.

A “Probe Reagent Reconstitution Solution” contains 100 mM succinic acid,73 mM lithium lauryl sulfate, 100 mM lithium hydroxide monohydrate, 15mM aldrithiol, 1.2 M lithium chloride, 20 mM EDTA, 3% (v/v) ethylalcohol, and 2M lithium hydroxide to pH 4.7.

A “Selection Reagent” contains 600 mM boric acid, ACS, 182.5 mM sodiumhydroxide, ACS, 1% (v/v) TRITON X-100 detergent, and 4 M sodiumhydroxide to pH 8.5.

A “Detection Reagent” comprises Detect Reagent I, which contains 1 mMnitric acid and 32 mM hydrogen peroxide, 30% (v/v), and Detect ReagentII, which contains 1.5 M sodium hydroxide.

An “Oil Reagent” is a silicone oil.

EXAMPLE 2 Initial Amplification Oligonucleotide ConcentrationOptimization

In this example, two amplification oligonucleotides (SEQ ID NOs. 15 and18) specific for Megasphaera elsdenii were tested at three differentconcentrations (10, 20, 30 picomoles (pmol) per reaction) using 0, 1,10, 100, 1000, and 10000 colony forming units (CFU) of M. elsdenii cells(ATCC No. 17752) per milliliter (mL) of Lysis Buffer. The first 27 basesof SEQ ID NO: 18 was a T7 promoter sequence. Additional oligonucleotidesincluded two target capture probes (SEQ ID NOs. 1 and 2) and a detectionprobe (SEQ ID NO:24 with an acridinium esther (AE) incorporated using alinker positioned between bases 11 and 12). The amplificationoligonucleotides were evaluated using (1) Target Capture, described inWeisburg et al., U.S. Pat. No. 6,110,678 (the contents of which areincorporated by reference herein); (2) Transcription-MediatedAmplification (TMA), described in Kacian et al. in U.S. Pat. Nos.5,399,491 and 5,480,784 (the contents of which are incorporated byreference herein) and by Lee et al., supra, ch. 8; and (3) HybridizationProtection Assay (HPA), described in Arnold et al., U.S. Pat. No.5,283,174 (the contents of which are incorporated by reference herein).The protocols for each method are briefly described below.

Megasphaera elsdenii were lysed in Lysis Buffer and diluted with LysisBuffer to 10000, 1000, 100, 1, and 0 CFU per mL and 400 μL of eachconcentration were placed in separate 12 mm×75 mm tubes. Target CaptureReagent, 100 μL containing 2 picomoles (pmol) of SEQ ID Nos. 1 and 2,was added to each tube and the tubes were covered and incubated at 62°C. for 30 minutes to immobilize the IVT, if present, on the magneticbeads. The magnetic beads were pelleted using a DTS® 400 Target CaptureSystem (Gen-Probe; Cat. No. 104555) and the supernatant was aspirated.The magnetic beads were resuspended in 1 mL of Wash Solution,re-pelletted and the Wash Solution was aspirated. The magnetic beadswere resuspended in 75 μL of reconstituted Amplification Reagentcontaining 10, 20, or 30 pmol of SEQ ID NOs. 15 and 18. Oil Reagent (200μL) was added to prevent evaporation and the tubes were covered andincubated at 62° C. for 10 minutes to disrupt secondary structures ofthe transcripts and allow the primer to bind. The tubes were thenincubated at 42° C. for 5 minutes to bring them to the appropriatetemperature for the enzymes. Reconstituted Enzyme Reagent (25 μL) wasadded and the tubes were incubated at 42° C. for 60 minutes to allow theenzymes to amplify the target nucleic acid. Probe Reagent (100 μL)containing Xe6 RLU of the detection probe (SEQ ID NO:24 with anacridinium esther (AE) incorporated using a linker positioned betweenbases 11 and 12) was added to each tube. The tubes were brieflyvortexed, covered, and incubated at 62° C. for 20 minutes to allow theprobe to hybridize to the amplified nucleic acid. The tubes wereincubated at room temperature for 5 minutes. Label on the non-hybridizedprobes was inactivated by adding 250 μL of Selection Reagent andincubating at 62° C. for 10 minutes. The tubes were cooled at roomtemperature for 15 minutes. The tubes were analyzed in a LEADER®luminometer capable of automatically injecting 200 μL of Detect ReagentI, followed by 200 μL of Detect Reagent II, and then repeatedly readingthe emission light in the tubes. Five replicates were run for eachprimer concentration at each M. elsdenii concentration. The results weremeasured in relative light units (RLU) and a minimum of 100,000 RLU wasthe threshold for a test to be considered positive. The results aresummarized in Table 1, below and indicate an increase in primerconcentration increased the sensitivity of the assay.

TABLE 1 Amt. of M. elsdenii Amt. of Primer Ave. RFU % CV 0 CFU/mL 10pmol/rxn 6,246 59.3 1 CFU/mL 10 pmol/rxn 11,996 15.9 10 CFU/mL 10pmol/rxn 121,215 36.8 100 CFU/mL 10 pmol/rxn 26,931 21.1 1000 CFU/mL 10pmol/rxn 45,251 14.4 10000 CFU/mL 10 pmol/rxn 118,891 16.5 0 CFU/mL 20pmol/rxn 3,332 7.6 1 CFU/mL 20 pmol/rxn 14,358 17.7 10 CFU/mL 20pmol/rxn 30,982 54.6 100 CFU/mL 20 pmol/rxn 58,673 22.6 1000 CFU/mL 20pmol/rxn 137,117 3.1 10000 CFU/mL 20 pmol/rxn 376,183 9.1 0 CFU/mL 30pmol/rxn 3,654 7.5 1 CFU/mL 30 pmol/rxn 14,575 39.2 10 CFU/mL 30pmol/rxn 33,111 38.2 100 CFU/mL 30 pmol/rxn 113,825 29.9 1000 CFU/mL 30pmol/rxn 310,468 14.4 10000 CFU/mL 30 pmol/rxn 656,873 7.8

EXAMPLE 3 Refined Amplification Oligonucleotide ConcentrationOptimization

In this example, the concentrations of the two amplificationoligonucleotides (SEQ ID NOs. 15 and 18) described in Example 2 werefurther optimized. The target capture probes, detection probe, andprocedures were also the same as those described in Example 2. Theconcentration of each amplification oligonucleotide ranged from 12 pmolper reaction to 53 pmol per reaction. The amplification oligonucleotideswere evaluated using M. elsdenii cells (ATCC No. 17752) at 1000 CFU permL of Lysis Buffer. The negative control contained 30 pmol per reactionof each amplification oligonucleotide and Lysis Buffer without anybacteria cells. Five replicates were tested for each prime concentrationcombination and ten replicates were tested for the negative control. Theresults are summarized in Table 2, below and indicate that the optimalprimer concentrations were 22.5 pmol per reaction for SEQ ID NO:18 and53 pmol per reaction for SEQ ID NO:15.

TABLE 2 Amt. SEQ ID NO: 15 Amt. SEQ ID NO: 18 Ave. RFU % CV NegativeControl 4,893 10.8 15 pmol/rxn 15 pmol/rxn 213,098 23.5 15 pmol/rxn 30pmol/rxn 773,957 16.1 30 pmol/rxn 15 pmol/rxn 96,793 25.2 30 pmol/rxn 30pmol/rxn 508,003 2433 22.5 pmol/rxn 19 pmol/rxn 171,179 1539 22.5pmol/rxn 53 pmol/rxn 1,997,576 11.4 11.89 pmol/rxn 14 pmol/rxn 120,37523.5 33.11 pmol/rxn 14 pmol/rxn 76,395 21.8 22.5 pmol/rxn 22.5pmol/rxn   215,109 19.1

EXAMPLE 4 Sensitivity

In this example, the sensitivity of two capture probes (SEQ ID NOs. 1and 2), two amplification oligonucleotides (SEQ ID Nos. 15 and 18), anda detection probe (SEQ ID NO:24 with an AE incorporated using a linkerpositioned between bases 11 and 12) was evaluated using 0, 0.1, 1, 10,100, and 1000 CFU per mL of M. elsdenii cells. The procedures were thesame as those described in Example 2 with the following changes. Theconcentration of SEQ ID NO:15 was 50 pmol per reaction and theconcentration of SEQ ID NO:18 was 20 pmol per reaction. The results aresummarized in Table 3, below and indicate that the set ofoligonucleotides were able to detect 100 CFU per mL of M. elsdeniicells.

TABLE 3 Amt. M. elsdenii Ave. RFU % CV 0 CFU/mL 3265 11.2 0.1 CFU/mL15391 64.7 1 CFU/mL 46316 59.9 10 CFU/mL 141055 37.3 100 CFU/mL 3859026.2 1000 CFU/mL 820594 6.3

EXAMPLE 5 Spiked Clinical Samples

In this example, the ability of two capture probes (SEQ ID Nos. 1 and2), two amplification oligonucleotides (SEQ ID Nos. 15 and 18), and adetection probe (SEQ ID NO:24 with an AE incorporated using a linkerpositioned between bases 11 and 12) to detect M. elsdenii cells spikedinto clinical samples was evaluated. Swab samples were collected fromfemale volunteers and stored in Lysis Buffer. The swab samples wereinitially screened for X and divided into two pools based on the initialscreening. The pooled samples were spiked with M. elsdenii cells at 0,1, 10, 100, and 1000 CFU per mL. The procedures were the same as thosedescribed in Example 2 with the following changes. The concentration ofSEQ ID NO:15 was 50 pmol per reaction and the concentration of SEQ IDNO:18 was 20 pmol per reaction. The results are summarized in Table 4,below and indicate that the set of oligonucleotides were able to detect100 CFU per mL of M. elsdenii cells spiked into clinical samples.

TABLE 4 Pool Amt. M. elsdenii Ave. RFU % CV 1 0 40,587 71.2 1 27,31315.7 10 124,071 48.6 100 277,937 35.6 100 751,671 5.3 2 0 34,479 24.0 135,774 34.4 10 53,906 11.3 100 204,007 8.7 100 796,224 3.7

From the foregoing, it will be appreciated that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention. Accordingly, the invention is notlimited except as by the appended claims. All publications, patents, andpatent applications cited herein are hereby incorporated by reference intheir entireties for all purposes.

EXAMPLE 5 Exemplary Oligomer Sequences

In this example, there is provided a list of oligonucleotide sequencesdrafted with a 5′ to 3′ in orientation. (Table 5). Underlined sequencetext represents exemplary tail sequences configured to hybridize with animmobilized probe. Bolded sequence text represents exemplary promotersequences for promoter-based amplification oligomers. Pseudotarget (hasprimer binding sites but no probe binding sites).

TABLE 5 SEQ ID NO: Sequence Description  1CTACTGCTGCCTCCCGTAGGAGTTTAAAAA Target  AAAAAAAAAAAAAAAAAAAAAAAAA captureoligomer (univer-  sal - also captures Atopobium vaginae)  2GGACTACCAGGGTATCTAATCCTGTTTAAA Target  AAAAAAAAAAAAAAAAAAAAAAAAAAAcapture oligomer (univer-  sal - also captures Atopobium vaginae)  3CGACACGAGCTGACGACAGCCATGCATTTA Target  AAAAAAAAAAAAAAAAAAAAAAAAAAAAAcapture oligomer  4 GACGTCATCCCCACCTTCCTTTTAAAAAAA Target AAAAAAAAAAAAAAAAAAAAAAA capture oligomer  5CGTATTCGGTATTAGCAGCCGTTTAAAAAA Target  AAAAAAAAAAAAAAAAAAAAAAAA captureoligomer  6 GCTGGCACGTAGTTAGCCGTGGCTTTTAAA Target AAAAAAAAAAAAAAAAAAAAAAAAAAA capture oligomer  7 CTACTGCTGCCTCCCGTAGGAGTarget hybridizing sequence  (THS for SEQ ID  NO: 1)  8GGACTACCAGGGTATCTAATCCTG Target hybridizing sequence  (THS for SEQ ID NO: 2)  9 CGACACGAGCTGACGACAGCCATGCA Target hybridizing sequence (THS for SEQ ID  NO: 3) 10 GACGTCATCCCCACCTTCCT Target hybridizingsequence  (THS for SEQ ID  NO: 4) 11 CGTATTCGGTATTAGCAGCCG Targethybridizing sequence  (THS for SEQ ID  NO: 5) 12GCTGGCACGTAGTTAGCCGTGGCT Target hybridizing sequence  (THS for SEQ ID NO: 6) 13 GTAACGGCCCAACAAGGCGA Non-T7  primer 14 GCCCAACAAGGCGATGATCAGNon-T7  primer 15 CTGTTATACGGGACGAAT Non-T7  primer 16AATTTAATACGACTCACTATAGGGAGAGTA T7 amp  GGAGTCTGGGCCGTGTCTCAG oligo 17AATTTAATACGACTCACTATAGGGAGACGT T7 amp  AGGAGTCTGGGCCGTGTCTC oligo 18AATTTAATACGACTCACTATAGGGAGACCG T7 amp  CACTTTTAAGACCGACTTA oligo 19GTAGGAGTCTGGGCCGTGTCTCAG Target hybridizing sequence  (THS for SEQ ID NO: 16) 20 CGTAGGAGTCTGGGCCGTGTCTC Target hybridizing sequence  (THS forSEQ ID  NO: 17) 21 CCGCACTTTTAAGACCGACTTA Target hybridizing sequence (THS for SEQ ID  NO: 18) 22 AATTTAATACGACTCACTATAGGGAGA T7 promotersequence 23 CAGTAGCCGGTCTGAGAGGATGA Detection  probe 24GACGGTACCGTAAGAGAAAGCC Detection  probe 25 GTAGCCGGTCTGAGAGGATGAACGDetection  probe 26 CGGTACCGTAAGAGAAAG Detection  probe 27CTGTTATACGGGACGAATTAAGTCGGTCTT Pseudo- AAAAGTGCGG target 28GCCCARCAAGGCGA Core  primer sequence 29 GTNACGGCCCARCAAGGCGAKGATCAGPrimer  regions 30 GTAGCCGGTCTGAGAGGATGA Core probe sequence 31CAGTAGCCGGTCTGAGAGGATGAACG Probe  region 32 GTAGGAGTNTGGGCCGTGTCTC Core primer sequence 33 CGTAGGAGTNTGGGCCGTGTCTCAG Primer  region 34AGTTGGAGGGGTAACGGCCCAACAAGGCGA Extended  TGATCAG primer region 35GAGTNTGGGCCGTG Truncated  core primer  sequence 36CCTCCCGTAGGAGTNTGGGCCGTGTCTCAG Extended  TCCC primer region 37CTGTTATACGGGAC Core primer sequence 38 GGTTGTAAAGTTCTGTTATACGGGACGAATPrimer  GG region 39 CTTTTAAGACCGAC Core primer sequence 40GCCCCGCACTTTTAAGACCGACTTACGACG Primer  C region 41GTAACGGCCCAACAAGGCGACTGAGACACG Pseudo- GCCCAGACTCCTAC target 42GTAACGGCCCAACAAGGCGAGAGACACGGC Pseudo- CCAGACTCCTACG target 43GCCCAACAAGGCGATGATCAGCTGAGACAC Pseudo- GGCCCAGACTCCTAC target 44GCCCAACAAGGCGATGATCAGGAGACACGG Pseudo- CCCAGACTCCTACG target

What is claimed is:
 1. A combination of at least two oligomers fordetecting in a sample a Megasphaera sp. 16S rRNA or a gene encoding aMegasphaera sp.16S rRNA, said oligomer combination comprising: for afirst Megasphaera target region, a first amplification oligomercomprising a first target-hybridizing sequence that is from about 15 toabout 25 contiguous nucleotides contained in the sequence of SEQ IDNO:34 and that includes at least the sequence of SEQ ID NO:28; and asecond amplification oligomer comprising a second target-hybridizingsequence that is from about 15 to about 25 contiguous nucleotidescontained in the sequence of SEQ ID NO:36 and that includes at least thesequence of SEQ ID NO:35, and wherein the second amplification oligomeris a promoter primer further comprising a promoter sequence located 5′to the target-hybridizing sequence.
 2. (canceled)
 3. The combination ofat least two oligomers of claim 1, wherein the first target-hybridizingsequence has the sequence shown in SEQ ID NO:13 or SEQ ID NO:14.
 4. Thecombination of at least two oligomers of claim 1, wherein the secondtarget-hybridizing sequence is contained in the sequence of SEQ ID NO:33and includes at least the sequence of SEQ ID NO:32. 5-9. (canceled) 10.The combination of at least two oligomers of claim 1, wherein thepromoter sequence is a T7 promoter sequence.
 11. (canceled)
 12. Thecombination of at least two oligomers of claim 10, wherein the secondamplification oligomer has the sequence shown in SEQ ID NO:16 or SEQ IDNO:17. 13-20. (canceled)
 21. The combination of at least two oligomersof claim 1, further comprising at least one detection probe oligomercomprising a target-hybridizing sequence that is from about 14 to about40 nucleotides in length and is configured to specifically hybridize toa target sequence contained within the sequence of SEQ ID NO:31 andincludes at least the sequence of SEQ ID NO:30.
 22. (canceled)
 23. Thecombination of at least two oligomers of claim 21, wherein the detectionprobe target-hybridizing sequence is selected from the group consistingof SEQ ID NO:23 and SEQ ID NO:25. 24-30. (canceled)
 31. A kit comprisingthe combination of at least two oligomers as in claim
 1. 32. (canceled)33. A method for detecting in a sample a Megasphaera sp. target nucleicacid, wherein the target nucleic acid is a Megasphaera sp. 16S rRNA or agene encoding said 16S rRNA, said method comprising: (a) providing asample, wherein said sample is suspected of containing a Megasphaera sp.bacterium; (b) contacting said sample with at least two oligomers foramplifying a Megasphaera sp. nucleic acid target region corresponding tothe target nucleic acid, said oligomer combination comprising for afirst Megasphaera target region, a first amplification oligomercomprising a first target-hybridizing sequence that is from about 15 toabout 25 contiguous nucleotides contained in the sequence of SEQ IDNO:34 and that includes at least the sequence of SEQ ID NO:28; and asecond amplification oligomer comprising a second target-hybridizingsequence that is from about 15 to about 25 contiguous nucleotidescontained in the sequence of SEQ ID NO:36 and that includes at least thesequence of SEQ ID NO:35, and wherein the second amplification oligomeris a promoter primer further comprising a promoter sequence located 5′to the target-hybridizing sequence; (c) performing an in vitro nucleicacid amplification reaction, wherein any Megasphaera target nucleic acidpresent in said sample is used as a template for generating anamplification product; and (d) detecting the presence or absence of theamplification product, thereby indicating the presence or absence ofMegasphaera sp. in said sample, wherein the detecting step comprisescontacting said in vitro nucleic acid amplification reaction with adetection probe oligomer configured to specifically hybridize to theamplification product under conditions whereby the presence or absenceof the amplification product is determined, thereby indicating thepresence or absence of Megasphaera sp. in said sample.
 34. (canceled)35. The method of claim 33, wherein the first target-hybridizingsequence has the sequence shown in SEQ ID NO:13 or SEQ ID NO:14.
 36. Themethod of claim 33, wherein the second target-hybridizing sequence iscontained in the sequence of SEQ ID NO:33 and includes at least thesequence of SEQ ID NO:32.
 37. (canceled)
 38. The method of claim 33,wherein the second target-hybridizing sequence has the sequence shown inSEQ ID NO:19 or SEQ ID NO:20. 39-41. (canceled)
 42. The method of claim33, wherein the promoter sequence is a T7 promoter sequence. 43.(canceled)
 44. The method of claim 33, wherein the second amplificationoligomer has the sequence shown in SEQ ID NO:16 or SEQ ID NO:17. 45-48.(canceled)
 49. The method of any of claim 33, further comprisingpurifying the Megasphaera target nucleic acid from other components inthe sample before step (b).
 50. The method of claim 49, wherein thepurifying step comprises contacting the sample with at least one captureprobe oligomer comprising a target-hybridizing sequence covalentlyattached to a sequence or moiety that binds to an immobilized probe,wherein said target- hybridizing sequence is selected from the groupconsisting of SEQ ID NOs:7-12. 51-55. (canceled)
 56. The method of claim33 for the first Megasphaera target region, wherein the detection probeoligomer comprises a target-hybridizing sequence that is from about 14to about 40 nucleotides in length and is configured to specificallyhybridize to a target sequence contained within the sequence of SEQ IDNO:31 and includes at least the sequence of SEQ ID NO:30.
 57. (canceled)58. The method of claim 56, wherein the detection probetarget-hybridizing sequence is selected from the group consisting of SEQID NO:23 and SEQ ID NO:25. 59-65. (canceled)
 66. The method of claim 33,wherein the detection probe comprises a label selected from the groupconsisting of (a) a chemiluminescent label; (b) a fluorescent label; (c)a quencher; and (d) a combination of two or more labels, wherein each ofthe two or more labels is independently selected from (a), (b), or (c).67. The method of claim 33, wherein the detecting step (d) occurs duringthe amplifying step (c). 68-72. (canceled)
 73. The method of claim 33,wherein the amplification reaction at step (c) is an isothermalamplification reaction. 74-87. (canceled)